1
|
Mahendran TR, Cynthia B, Thevendran R, Maheswaran S. Prospects of Innovative Therapeutics in Combating the COVID-19 Pandemic. Mol Biotechnol 2024:10.1007/s12033-024-01240-4. [PMID: 39085563 DOI: 10.1007/s12033-024-01240-4] [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: 01/19/2024] [Accepted: 07/03/2024] [Indexed: 08/02/2024]
Abstract
The sudden global crisis of COVID-19, driven by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), demands swift containment measures due to its rapid spread and numerous problematic mutations, which complicate the establishment of herd immunity. With escalating fatalities across various nations no foreseeable end in sight, there is a pressing need to create swiftly deployable, rapid, cost-effective detection, and treatment methods. While various steps are taken to mitigate the transmission and severity of the disease, vaccination is proven throughout mankind history as the best method to acquire immunity and circumvent the spread of infectious diseases. Nonetheless, relying solely on vaccination might not be adequate to match the relentless viral mutations observed in emerging variants of SARS-CoV-2, including alterations to their RBD domain, acquisition of escape mutations, and potential resistance to antibody binding. Beyond the immune system activation achieved through vaccination, it is crucial to develop new medications or treatment methods to either impede the infection or enhance existing treatment modalities. This review emphasizes innovative treatment strategies that aim to directly disrupt the virus's ability to replicate and spread, which could play a role in ending the SARS-CoV-2 pandemic.
Collapse
Affiliation(s)
- Thamby Rajah Mahendran
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Binsin Cynthia
- School of Biological Sciences, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia
| | - Ramesh Thevendran
- Centre of Excellence for Nanobiotechnology & Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
- Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia
| | - Solayappan Maheswaran
- Centre of Excellence for Nanobiotechnology & Nanomedicine (CoExNano), Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia.
- Faculty of Applied Sciences, AIMST University, 08100, Bedong, Kedah, Malaysia.
| |
Collapse
|
2
|
Ferrer-Orta C, Vázquez-Monteagudo S, Ferrero DS, Martínez-González B, Perales C, Domingo E, Verdaguer N. Point mutations at specific sites of the nsp12-nsp8 interface dramatically affect the RNA polymerization activity of SARS-CoV-2. Proc Natl Acad Sci U S A 2024; 121:e2317977121. [PMID: 38990941 PMCID: PMC11260105 DOI: 10.1073/pnas.2317977121] [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: 10/16/2023] [Accepted: 06/04/2024] [Indexed: 07/13/2024] Open
Abstract
In a recent characterization of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variability present in 30 diagnostic samples from patients of the first COVID-19 pandemic wave, 41 amino acid substitutions were documented in the RNA-dependent RNA polymerase (RdRp) nsp12. Eight substitutions were selected in this work to determine whether they had an impact on the RdRp activity of the SARS-CoV-2 nsp12-nsp8-nsp7 replication complex. Three of these substitutions were found around the polymerase central cavity, in the template entry channel (D499G and M668V), and within the motif B (V560A), and they showed polymerization rates similar to the wild type RdRp. The remaining five mutations (P323L, L372F, L372P, V373A, and L527H) were placed near the nsp12-nsp8F contact surface; residues L372, V373, and L527 participated in a large hydrophobic cluster involving contacts between two helices in the nsp12 fingers and the long α-helix of nsp8F. The presence of any of these five amino acid substitutions resulted in important alterations in the RNA polymerization activity. Comparative primer elongation assays showed different behavior depending on the hydrophobicity of their side chains. The substitution of L by the bulkier F side chain at position 372 slightly promoted RdRp activity. However, this activity was dramatically reduced with the L372P, and L527H mutations, and to a lesser extent with V373A, all of which weaken the hydrophobic interactions within the cluster. Additional mutations, specifically designed to disrupt the nsp12-nsp8F interactions (nsp12-V330S, nsp12-V341S, and nsp8-R111A/D112A), also resulted in an impaired RdRp activity, further illustrating the importance of this contact interface in the regulation of RNA synthesis.
Collapse
Affiliation(s)
- Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| | - Diego S. Ferrero
- Structural and Molecular Biology Department, Institut de Biologia 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
| | - 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
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biologia Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona08028, Spain
| |
Collapse
|
3
|
Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [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: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
Collapse
Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
| |
Collapse
|
4
|
Nonaka CKV, de Jesus Ribeiro AM, Rocha GV, da Hora HS, Junior AAF, Lima FDM, Bastos IN, Teles SAS, Weber TGL, Costa VF, Costa-Ferro ZS, Rocha CAG, Sardi SI, Soares G, Mendes AVA, Souza BSDF. Assessing the Clinical Impact of the SARS-CoV-2 Gamma Variant on Intensive Care Unit Admissions: Insights from a Reference Hospital in Northeastern Brazil. Viruses 2024; 16:467. [PMID: 38543835 PMCID: PMC10974300 DOI: 10.3390/v16030467] [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: 12/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 05/23/2024] Open
Abstract
The global challenge posed by the prolonged COVID-19 pandemic underscores the critical need for ongoing genomic surveillance to identify emerging variants and formulate effective public health strategies. This retrospective observational study, conducted in a reference hospital in Northeast Brazil and comprising 2116 cases, employed PCR genotyping together with epidemiological data to elucidate the impact of the Gamma variant during its emergence, revealing distinct patterns in hospitalization rates, severity of illness, and outcomes. The study emphasizes the challenges posed by the variant, particularly an increased tendency for ICU admissions and respiratory support, especially among adults aged 18 to 59 without comorbidities. Laboratory analyses further demonstrate elevated inflammatory, coagulation, and hepatic markers in the Gamma variant cohort, suggesting a more severe systemic response. Despite limitations, including a retrospective approach and single-institution data, the study underscores the importance of ongoing genomic surveillance. Overall, this research contributes valuable insights into the impact of the Gamma variant on COVID-19 dynamics, advocating for continued research and surveillance to inform effective public health strategies regarding evolving viral variants.
Collapse
Affiliation(s)
- Carolina Kymie Vasques Nonaka
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | | | - Gisele Vieira Rocha
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
| | - Helena Souza da Hora
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | | | | | - Iasmin Nogueira Bastos
- Faculty of Medicine and Dentistry, Federal University of Bahia, Salvador 40110-100, BA, Brazil;
| | - Samara Alves Sa Teles
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | | | - Vanessa Ferreira Costa
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | - Zaquer Suzana Costa-Ferro
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
| | - Clarissa Araújo Gurgel Rocha
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
- Faculty of Medicine and Dentistry, Federal University of Bahia, Salvador 40110-100, BA, Brazil;
| | - Silvia Inês Sardi
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | - Gúbio Soares
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | | | - Bruno Solano de Freitas Souza
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
| |
Collapse
|
5
|
Fournelle D, Mostefai F, Brunet-Ratnasingham E, Poujol R, Grenier JC, Gálvez JH, Pagliuzza A, Levade I, Moreira S, Benlarbi M, Beaudoin-Bussières G, Gendron-Lepage G, Bourassa C, Tauzin A, Grandjean Lapierre S, Chomont N, Finzi A, Kaufmann DE, Craig M, Hussin JG. Intra-Host Evolution Analyses in an Immunosuppressed Patient Supports SARS-CoV-2 Viral Reservoir Hypothesis. Viruses 2024; 16:342. [PMID: 38543708 PMCID: PMC10974702 DOI: 10.3390/v16030342] [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: 01/26/2024] [Revised: 02/17/2024] [Accepted: 02/20/2024] [Indexed: 05/23/2024] Open
Abstract
Throughout the SARS-CoV-2 pandemic, several variants of concern (VOCs) have been identified, many of which share recurrent mutations in the spike glycoprotein's receptor-binding domain (RBD). This region coincides with known epitopes and can therefore have an impact on immune escape. Protracted infections in immunosuppressed patients have been hypothesized to lead to an enrichment of such mutations and therefore drive evolution towards VOCs. Here, we present the case of an immunosuppressed patient that developed distinct populations with immune escape mutations throughout the course of their infection. Notably, by investigating the co-occurrence of substitutions on individual sequencing reads in the RBD, we found quasispecies harboring mutations that confer resistance to known monoclonal antibodies (mAbs) such as S:E484K and S:E484A. These mutations were acquired without the patient being treated with mAbs nor convalescent sera and without them developing a detectable immune response to the virus. We also provide additional evidence for a viral reservoir based on intra-host phylogenetics, which led to a viral substrain that evolved elsewhere in the patient's body, colonizing their upper respiratory tract (URT). The presence of SARS-CoV-2 viral reservoirs can shed light on protracted infections interspersed with periods where the virus is undetectable, and potential explanations for long-COVID cases.
Collapse
Affiliation(s)
- Dominique Fournelle
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Fatima Mostefai
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Elsa Brunet-Ratnasingham
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Raphaël Poujol
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - Jean-Christophe Grenier
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
| | - José Héctor Gálvez
- Canadian Centre for Computational Genomics, Montréal, QC H3A 0G1, Canada;
| | - Amélie Pagliuzza
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Inès Levade
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Sandrine Moreira
- Laboratoire de Santé Publique du Québec, Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC H9X 3R5, Canada; (I.L.)
| | - Mehdi Benlarbi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Gabrielle Gendron-Lepage
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Catherine Bourassa
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
| | - Alexandra Tauzin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Simon Grandjean Lapierre
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Andrés Finzi
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
| | - Daniel E. Kaufmann
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montréal, QC H2X 0A9, Canada; (E.B.-R.); (A.P.); (M.B.); (G.B.-B.); (G.G.-L.); (C.B.); (A.T.); (S.G.L.); (N.C.); (D.E.K.)
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC H2X 0C1, Canada
- Division of Infectious Diseases, Department of Medicine, University Hospital and University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Morgan Craig
- Research Centre, Centre Hospitalier UniversitaireSainte-Justine, Montréal, QC H3T 1C5, Canada;
- Département de Mathématiques et de Statistique, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Julie G. Hussin
- Research Centre Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; (D.F.); (F.M.); (R.P.); (J.-C.G.)
- Département de Médecine, Université de Montréal, Montréal, QC H3C 3J7, Canada
- Mila-Quebec AI Institute, Montréal, QC H2S 3H1, Canada
| |
Collapse
|
6
|
Ahmed N, Athavale A, Tripathi AH, Subramaniam A, Upadhyay SK, Pandey AK, Rai RC, Awasthi A. To be remembered: B cell memory response against SARS-CoV-2 and its variants in vaccinated and unvaccinated individuals. Scand J Immunol 2024; 99:e13345. [PMID: 38441373 DOI: 10.1111/sji.13345] [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: 06/01/2023] [Revised: 10/20/2023] [Accepted: 11/13/2023] [Indexed: 03/07/2024]
Abstract
COVID-19 disease has plagued the world economy and affected the overall well-being and life of most of the people. Natural infection as well as vaccination leads to the development of an immune response against the pathogen. This involves the production of antibodies, which can neutralize the virus during future challenges. In addition, the development of cellular immune memory with memory B and T cells provides long-lasting protection. The longevity of the immune response has been a subject of intensive research in this field. The extent of immunity conferred by different forms of vaccination or natural infections remained debatable for long. Hence, understanding the effectiveness of these responses among different groups of people can assist government organizations in making informed policy decisions. In this article, based on the publicly available data, we have reviewed the memory response generated by some of the vaccines against SARS-CoV-2 and its variants, particularly B cell memory in different groups of individuals.
Collapse
Affiliation(s)
- Nafees Ahmed
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Atharv Athavale
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Ankita H Tripathi
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | - Adarsh Subramaniam
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Santosh K Upadhyay
- Department of Biotechnology, Kumaun University, Nainital, Uttarakhand, India
| | | | - Ramesh Chandra Rai
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| | - Amit Awasthi
- Translational Health Science and Technology Institute, Faridabad, Haryana, India
| |
Collapse
|
7
|
Freitas MTDS, Sena LOC, Fukutani KF, dos Santos CA, Neto FDCB, Ribeiro JS, dos Reis ES, Balbino VDQ, de Sá Paiva Leitão S, de Aragão Batista MV, Lipscomb MW, de Moura TR. The increase in SARS-CoV-2 lineages during 2020-2022 in a state in the Brazilian Northeast is associated with a number of cases. Front Public Health 2023; 11:1222152. [PMID: 38186707 PMCID: PMC10771345 DOI: 10.3389/fpubh.2023.1222152] [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: 05/13/2023] [Accepted: 11/15/2023] [Indexed: 01/09/2024] Open
Abstract
SARS-CoV-2 has caused a high number of deaths in several countries. In Brazil, there were 37 million confirmed cases of COVID-19 and 700,000 deaths caused by the disease. The population size and heterogeneity of the Brazilian population should be considered in epidemiological surveillance due to the varied tropism of the virus. As such, municipalities and states must be factored in for their unique specificities, such as socioeconomic conditions and population distribution. Here, we investigate the spatiotemporal dispersion of emerging SARS-CoV-2 lineages and their dynamics in each microregion from Sergipe state, northeastern Brazil, in the first 3 years of the pandemic. We analyzed 586 genomes sequenced between March 2020 and November 2022 extracted from the GISAID database. Phylogenetic analyses were carried out for each data set to reconstruct evolutionary history. Finally, the existence of a correlation between the number of lineages and infection cases by SARS-CoV-2 was evaluated. Aracaju, the largest city in northeastern Brazil, had the highest number of samples sequenced. This represented 54.6% (320) of the genomes, and consequently, the largest number of lineages identified. Studies also analyzed the relationship between mean lineage distributions and mean monthly infections, daily cases, daily deaths, and hospitalizations of vaccinated and unvaccinated patients. For this, a correlation matrix was created. Results revealed that the increase in the average number of SARS-CoV-2 variants was related to the average number of SARS-CoV-2 cases in both unvaccinated and vaccinated individuals. Thus, our data indicate that it is necessary to maintain epidemiological surveillance, especially in capital cities, since they have a high rate of circulation of resident and non-resident inhabitants, which contributes to the dynamics of the virus.
Collapse
Affiliation(s)
- Moises Thiago de Souza Freitas
- Health Sciences Graduate Program, Federal University of Sergipe, Aracaju, Brazil
- Parasitic Biology Graduate Program, Federal University of Sergipe, São Cristóvão, Brazil
| | - Ludmila Oliveira Carvalho Sena
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | - Kiyoshi Ferreira Fukutani
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, NH, United States
| | - Cliomar Alves dos Santos
- Health Foundation Parreiras Horta, Central Laboratory of Public Health (LACEN/SE), Sergipe State Health Secretariat, Aracaju, Brazil
| | | | - Julienne Sousa Ribeiro
- Center for Biological and Health Sciences, Federal University of Sergipe, São Cristóvão, Brazil
| | | | | | | | | | | | | |
Collapse
|
8
|
Goswami B, Sarkar MMH, Akter S, Banu TA, Jahan I, Hossain MS, Uddin MM, Nafisa T, Molla MMA, Yeasmin M, Osman E, Uzzaman MS, Mahmud ASM, Habib A, Khan S. Emergence of SARS-CoV-2 variant of interest B.1.525 (Eta) in Bangladesh. Biologicals 2023; 84:101714. [PMID: 37804694 DOI: 10.1016/j.biologicals.2023.101714] [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: 10/11/2022] [Revised: 07/02/2023] [Accepted: 09/25/2023] [Indexed: 10/09/2023] Open
Abstract
In the present study, we report the complete genome of five Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) from Bangladesh harboring mutations at Spike protein (E484K, Q677H, D614G, A67V, Q52R, Y144del, H69del, V70del, F888L) assigned to the B.1.525 lineage (Variant of interest). Mutations are also found in viral structural proteins other than spike region (E_L21F, M_I82F, N_A12G and N_T208I) and other mutations (NSP3_T1189I, NSP6_S106del, NSP6_F108del, NSP6_G107del, NSP12_P323F) from all of five B.1.525 SARS-CoV-2 variants of Bangladesh. We have also found four unique mutations from two of SARS-CoV-2 B.1.525 variant of Bangladesh. Among the four unique mutations two mutations (NS7a_L96H, NS7a_Y97D) obtained from strain BCSIR-NILMRC-718, one (NSP3_A1430V) from BCSIR-NILMRC-738 and two mutation including one spike protein mutation (NSP2_L444I, Spike_I68 M) present in BCSIR-AFIP-10 strain. The identification of new mutations will contribute to characterizing SARS-CoV-2, to continue tracking its spread and better understanding its biological and clinical features to take medical countermeasures and vaccines.
Collapse
Affiliation(s)
- Barna Goswami
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | | | - Shahina Akter
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Tanjina Akhtar Banu
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Iffat Jahan
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Md Saddam Hossain
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Mohammad Mohi Uddin
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Tasnim Nafisa
- National Institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh.
| | - Md Maruf Ahmed Molla
- National Institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh.
| | - Mahmuda Yeasmin
- National Institute of Laboratory Medicine and Referral Center, Dhaka, Bangladesh.
| | - Eshrar Osman
- SciTech Consulting and Solutions, Dhaka, Bangladesh.
| | | | | | - Ahashan Habib
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| | - Salim Khan
- Bangladesh Council of Scientific and Industrial Research, Dhaka, Bangladesh.
| |
Collapse
|
9
|
Wang J, Zhang Y, Liu C, Zha W, Dong S, Wang Y, Jiang Y, Xing H, Li X. Trivalent mRNA Vaccine against SARS-CoV-2 and Variants with Effective Immunization. Mol Pharm 2023; 20:4971-4983. [PMID: 37699256 DOI: 10.1021/acs.molpharmaceut.2c00860] [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] [Indexed: 09/14/2023]
Abstract
mRNA vaccines encoding a single spike protein effectively prevent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. However, the emergence of SARS-CoV-2 variants leads to a wide range of immune evasion. Herein, a unique trivalent mRNA vaccine based on ancestral SARS-CoV-2, Delta, and Omicron variant spike receptor-binding domain (RBD) mRNAs was developed to tackle the immune evasion of the variants. First, three RBD mRNAs of SARS-CoV-2, Delta, and Omicron were coencapsulated into lipid nanoparticles (LNPs) by using microfluidic technology. After that, the physicochemical properties and time-dependent storage stability of the trivalent mRNA vaccine nanoformulation were tested by using dynamic light scattering (DLS). In vitro, the trivalent mRNA vaccine exhibited better lysosomal escape ability, transfection efficiency, and biocompatibility than did the commercial transfection reagent Lipo3000. In addition, Western blot analyses confirmed that the three RBD proteins can be detected in cells transfected with the trivalent mRNA vaccine. Furthermore, ex vivo imaging analysis indicated that the livers of BALB/c mice had the strongest protein expression levels after intramuscular (IM) injection. Using a prime-boost strategy, this trivalent vaccine elicited robust humoral and T-cell immune responses in both the high-dose and low-dose groups and showed no toxicity in BALB/c mice. Three specific IgG antibodies in the high-dose group against SARS-CoV-2, Delta, and Omicron variants approached ∼1/1,833,333, ∼1/1,866,667, and ∼1/925,000, respectively. Taken together, two doses of inoculation with the trivalent mRNA vaccine may provide broad and effective immunization responses against SARS-CoV-2 and variants.
Collapse
Affiliation(s)
- Ji Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yanhao Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Chao Liu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Wenhui Zha
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Shuo Dong
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yang Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Yuhao Jiang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Hanlei Xing
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| | - Xinsong Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 14122, PR China
| |
Collapse
|
10
|
Yu B, Cao L, Li S, Klauser PC, Wang L. The proximity-enabled sulfur fluoride exchange reaction in the protein context. Chem Sci 2023; 14:7913-7921. [PMID: 37502323 PMCID: PMC10370592 DOI: 10.1039/d3sc01921g] [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: 04/12/2023] [Accepted: 06/20/2023] [Indexed: 07/29/2023] Open
Abstract
The proximity-enabled sulfur(vi) fluoride exchange (SuFEx) reaction generates specific covalent linkages between proteins in cells and in vivo, which opens innovative avenues for studying elusive protein-protein interactions and developing potent covalent protein drugs. To exploit the power and expand the applications of covalent proteins, covalent linkage formation between proteins is the critical step, for which fundamental kinetic and essential properties remain unexplored. Herein, we systematically studied SuFEx kinetics in different proteins and conditions. In contrast to in small molecules, SuFEx in interacting proteins conformed with a two-step mechanism involving noncovalent binding, followed by covalent bond formation, exhibiting nonlinear rate dependence on protein concentration. The protein SuFEx rate consistently changed with protein binding affinity as well as chemical reactivity of the functional group and was impacted by target residue identity and solution pH. In addition, kinetic analyses of nanobody SR4 binding with SARS-CoV-2 spike protein revealed that viral target mutations did not abolish covalent binding but decreased the SuFEx rate with affinity decrease. Moreover, off-target cross-linking of a SuFEx-capable nanobody in human serum was not detected, and the SuFEx-generated protein linkage was stable at cellular acidic pHs, suggesting SuFEx suitability for in vivo usage. These results advanced our understanding of SuFEx reactivity and kinetics in proteins, which is invaluable for ongoing exploration of SuFEx-enabled covalent proteins for basic biological research and creative biotherapeutics.
Collapse
Affiliation(s)
- Bingchen Yu
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Li Cao
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Shanshan Li
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Paul C Klauser
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| | - Lei Wang
- Department of Pharmaceutical Chemistry, The Cardiovascular Research Institute, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco 555 Mission Bay Blvd. South San Francisco California 94158 USA
| |
Collapse
|
11
|
Franco-Luiz APM, Fernandes NMGS, Silva TBDS, Bernardes WPDOS, Westin MR, Santos TG, Fernandes GDR, Simões TC, Silva EFE, Gava SG, Alves BM, de Carvalho Melo M, da Silva-Pereira RA, Alves PA, Fonseca CT. Longitudinal study of humoral immunity against SARS-CoV-2 of health professionals in Brazil: the impact of booster dose and reinfection on antibody dynamics. Front Immunol 2023; 14:1220600. [PMID: 37520570 PMCID: PMC10376701 DOI: 10.3389/fimmu.2023.1220600] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/26/2023] [Indexed: 08/01/2023] Open
Abstract
Introduction The pandemic caused by SARS-CoV-2 has had a major impact on health systems. Vaccines have been shown to be effective in improving the clinical outcome of COVID-19, but they are not able to fully prevent infection and reinfection, especially that caused by new variants. Methods Here, we tracked for 450 days the humoral immune response and reinfection in 52 healthcare workers from Brazil. Infection and reinfection were confirmed by RT-qPCR, while IgM and IgG antibody levels were monitored by rapid test. Results Of the 52 participants, 19 (36%) got reinfected during the follow-up period, all presenting mild symptoms. For all participants, IgM levels dropped sharply, with over 47% of them becoming seronegative by the 60th day. For IgG, 90% of the participants became seropositive within the first 30 days of follow-up. IgG antibodies also dropped after this period reaching the lowest level on day 270 (68.5 ± 72.3, p<0.0001). Booster dose and reinfection increased the levels of both antibodies, with the interaction between them resulting in an increase in IgG levels of 130.3 arbitrary units. Conclusions Overall, our data indicate that acquired humoral immunity declines over time and suggests that IgM and IgG antibody levels are not associated with the prevention of reinfection.
Collapse
Affiliation(s)
- Ana Paula Moreira Franco-Luiz
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Nubia Monteiro Gonçalves Soares Fernandes
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Thais Bárbara de Souza Silva
- Grupo de Imunologia de Doenças Virais, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | | | - Mateus Rodrigues Westin
- Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Thais Garcia Santos
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel da Rocha Fernandes
- Grupo de Pesquisa em Informática de Biossistemas, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Taynãna César Simões
- Núcleo de Estudos em Saúde Pública e Envelhecimento, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Eduardo Fernandes E. Silva
- Serviço de capacitação em métodos quantitativos -SAMeQ, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Sandra Grossi Gava
- Grupo de Pesquisa em Helmintologia e Malacologia Médica, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Breno Magalhães Alves
- Centro de Vigilância em Saúde e Segurança do Paciente, Hospital Metropolitano Doutor Célio de Castro, Belo Horizonte, Minas Gerais, Brazil
| | - Mariana de Carvalho Melo
- Serviço Especializado em Segurança e Medicina do Trabalho, Hospital Metropolitano Doutor Célio de Castro, Belo Horizonte, Minas Gerais, Brazil
| | - Rosiane A. da Silva-Pereira
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Pedro Augusto Alves
- Grupo de Imunologia de Doenças Virais, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| | - Cristina Toscano Fonseca
- Grupo de Pesquisa em Biologia e Imunologia de Doenças Infecciosas e Parasitárias, Instituto René Rachou, Fundação Oswaldo Cruz, Belo Horizonte, Minas Gerais, Brazil
| |
Collapse
|
12
|
Khetran SR, Mustafa R. Mutations of SARS-CoV-2 Structural Proteins in the Alpha, Beta, Gamma, and Delta Variants: Bioinformatics Analysis. JMIR BIOINFORMATICS AND BIOTECHNOLOGY 2023; 4:e43906. [PMID: 37485046 PMCID: PMC10353769 DOI: 10.2196/43906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 03/02/2023] [Accepted: 06/08/2023] [Indexed: 07/25/2023]
Abstract
Background COVID-19 and Middle East Respiratory Syndrome are two pandemic respiratory diseases caused by coronavirus species. The novel disease COVID-19 caused by SARS-CoV-2 was first reported in Wuhan, Hubei Province, China, in December 2019, and became a pandemic within 2-3 months, affecting social and economic platforms worldwide. Despite the rapid development of vaccines, there have been obstacles to their distribution, including a lack of fundamental resources, poor immunization, and manual vaccine replication. Several variants of the original Wuhan strain have emerged in the last 3 years, which can pose a further challenge for control and vaccine development. Objective The aim of this study was to comprehensively analyze mutations in SARS-CoV-2 variants of concern (VoCs) using a bioinformatics approach toward identifying novel mutations that may be helpful in developing new vaccines by targeting these sites. Methods Reference sequences of the SARS-CoV-2 spike (YP_009724390) and nucleocapsid (YP_009724397) proteins were compared to retrieved sequences of isolates of four VoCs from 14 countries for mutational and evolutionary analyses. Multiple sequence alignment was performed and phylogenetic trees were constructed by the neighbor-joining method with 1000 bootstrap replicates using MEGA (version 6). Mutations in amino acid sequences were analyzed using the MultAlin online tool (version 5.4.1). Results Among the four VoCs, a total of 143 nonsynonymous mutations and 8 deletions were identified in the spike and nucleocapsid proteins. Multiple sequence alignment and amino acid substitution analysis revealed new mutations, including G72W, M2101I, L139F, 209-211 deletion, G212S, P199L, P67S, I292T, and substitutions with unknown amino acid replacement, reported in Egypt (MW533289), the United Kingdom (MT906649), and other regions. The variants B.1.1.7 (Alpha variant) and B.1.617.2 (Delta variant), characterized by higher transmissibility and lethality, harbored the amino acid substitutions D614G, R203K, and G204R with higher prevalence rates in most sequences. Phylogenetic analysis among the novel SARS-CoV-2 variant proteins and some previously reported β-coronavirus proteins indicated that either the evolutionary clade was weakly supported or not supported at all by the β-coronavirus species. Conclusions This study could contribute toward gaining a better understanding of the basic nature of SARS-CoV-2 and its four major variants. The numerous novel mutations detected could also provide a better understanding of VoCs and help in identifying suitable mutations for vaccine targets. Moreover, these data offer evidence for new types of mutations in VoCs, which will provide insight into the epidemiology of SARS-CoV-2.
Collapse
Affiliation(s)
- Saima Rehman Khetran
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
| | - Roma Mustafa
- Department of Life Sciences Sardar Bahadur Khan Women's University Quetta Pakistan
| |
Collapse
|
13
|
Sinha A, Sangeet S, Roy S. Evolution of Sequence and Structure of SARS-CoV-2 Spike Protein: A Dynamic Perspective. ACS OMEGA 2023; 8:23283-23304. [PMID: 37426203 PMCID: PMC10324094 DOI: 10.1021/acsomega.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 06/01/2023] [Indexed: 07/11/2023]
Abstract
Novel coronavirus (SARS-CoV-2) enters its host cell through a surface spike protein. The viral spike protein has undergone several modifications/mutations at the genomic level, through which it modulated its structure-function and passed through several variants of concern. Recent advances in high-resolution structure determination and multiscale imaging techniques, cost-effective next-generation sequencing, and development of new computational methods (including information theory, statistical methods, machine learning, and many other artificial intelligence-based techniques) have hugely contributed to the characterization of sequence, structure, function of spike proteins, and its different variants to understand viral pathogenesis, evolutions, and transmission. Laying on the foundation of the sequence-structure-function paradigm, this review summarizes not only the important findings on structure/function but also the structural dynamics of different spike components, highlighting the effects of mutations on them. As dynamic fluctuations of three-dimensional spike structure often provide important clues for functional modulation, quantifying time-dependent fluctuations of mutational events over spike structure and its genetic/amino acidic sequence helps identify alarming functional transitions having implications for enhanced fusogenicity and pathogenicity of the virus. Although these dynamic events are more difficult to capture than quantifying a static, average property, this review encompasses those challenging aspects of characterizing the evolutionary dynamics of spike sequence and structure and their implications for functions.
Collapse
|
14
|
Bettinger JA, Irvine MA, Shulha HP, Valiquette L, Muller MP, Vanderkooi OG, Kellner JD, Top KA, Sadarangani M, McGeer A, Isenor JE, Marty K, Soe P, De Serres G. Adverse Events Following Immunization With mRNA and Viral Vector Vaccines in Individuals With Previous Severe Acute Respiratory Syndrome Coronavirus 2 Infection From the Canadian National Vaccine Safety Network. Clin Infect Dis 2023; 76:1088-1102. [PMID: 36310514 PMCID: PMC9620384 DOI: 10.1093/cid/ciac852] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/17/2022] [Accepted: 10/26/2022] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND Adults previously infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop short-term immunity and may have increased reactogenicity to coronavirus disease 2019 (COVID-19) vaccines. This prospective, multicenter, active-surveillance cohort study examined the short-term safety of COVID-19 vaccines in adults with a prior history of SARS-CoV-2. METHODS Canadian adults vaccinated between 22 December 2020 and 27 November 2021 were sent an electronic questionnaire 7 days post-dose 1, dose 2, and dose 3 vaccination. The main outcome was health events occurring in the first 7 days after each vaccination that prevented daily activities, resulted in work absenteeism, or required a medical consultation, including hospitalization. RESULTS Among 684 998 vaccinated individuals, 2.6% (18 127/684 998) reported a prior history of SARS-CoV-2 infection a median of 4 (interquartile range: 2-6) months previously. After dose 1, individuals with moderate (bedridden) to severe (hospitalized) COVID-19 who received BNT162b2, mRNA-1273, or ChAdox1-S vaccines had higher odds of a health event preventing daily activities, resulting in work absenteeism or requiring medical consultation (adjusted odds ratio [95% confidence interval]: 3.96 [3.67-4.28] for BNT162b2, 5.01 [4.57-5.50] for mRNA-1273, and 1.84 [1.54-2.20] for ChAdox1-S compared with no infection). Following dose 2 and 3, the greater risk associated with previous infection was also present but was attenuated compared with dose 1. For all doses, the association was lower or absent after mild or asymptomatic infection. CONCLUSIONS Adults with moderate or severe previous SARS-CoV-2 infection were more likely to have a health event sufficient to impact routine activities or require medical assessment in the week following each vaccine dose.
Collapse
Affiliation(s)
- Julie A Bettinger
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | | | - Hennady P Shulha
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Louis Valiquette
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Canada
| | | | - Otto G Vanderkooi
- Department of Pediatrics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - James D Kellner
- Department of Pediatrics and Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Canada
| | - Karina A Top
- Canadian Center for Vaccinology, IWK Health and Department of Pediatrics, Dalhousie University, Halifax, Canada
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
- Department of Pediatrics, University of British Columbia, Vancouver, Canada
| | - Allison McGeer
- Sinai Health System and University of Toronto, Toronto, Canada
| | - Jennifer E Isenor
- College of Pharmacy and Canadian Center for Vaccinology, Dalhousie University, Halifax, Canada
| | - Kimberly Marty
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
| | - Phyumar Soe
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, Canada
| | - Gaston De Serres
- CHU de Québec-Université Laval, Quebec City, Canada
- Institut National de Santé Publique du Québec, Quebec City, Canada
| | | |
Collapse
|
15
|
Dermatological Manifestations in COVID-19: A Case Study of SARS-CoV-2 Infection in a Genetic Thrombophilic Patient with Mthfr Mutation. Pathogens 2023; 12:pathogens12030438. [PMID: 36986360 PMCID: PMC10058784 DOI: 10.3390/pathogens12030438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 12/23/2022] [Accepted: 01/18/2023] [Indexed: 03/16/2023] Open
Abstract
The present case study describes the dermatological manifestations of COVID-19 in a patient with genetic thrombophilia (MTHFR–C677T mutation) and the identification of a SARS-CoV-2 variant of interest (VOI). A female patient, 47 years old, unvaccinated, with thrombophilia, was diagnosed with COVID-19. She presented with urticarial and maculopapular eruptions from the seventh day of symptoms, which progressed to multiple lesions with dark centers (D-dimer value > 1450 ng/mL). The dermatological manifestations disappeared after 30 days, corroborating the reduction in D-dimer levels. Viral genome sequencing revealed infection by the VOI Zeta (P.2). Antibody testing, performed 30 days after the onset of symptoms, detected only IgG. The virus neutralization test showed the highest neutralizing titer for a P.2 strain, validating the genotypic identification. Lesions were suggested to be due to infection in skin cells causing a direct cytopathic effect or release of pro-inflammatory cytokines triggering erythematous and urticarial eruptions. In addition, vascular complications are also proposed to be due to the MTHFR mutation and increased D-dimer values. This case report is an alert about COVID-19 in patients with pre-existing vascular diseases, especially in unvaccinated patients, by VOI.
Collapse
|
16
|
A high-resolution melt curve toolkit to identify lineage-defining SARS-CoV-2 mutations. Sci Rep 2023; 13:3887. [PMID: 36890186 PMCID: PMC9994400 DOI: 10.1038/s41598-023-30754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 02/28/2023] [Indexed: 03/10/2023] Open
Abstract
The emergence of severe acute respiratory syndrome 2 (SARS-CoV-2) variants of concern (VOCs), with mutations linked to increased transmissibility, vaccine escape and virulence, has necessitated the widespread genomic surveillance of SARS-CoV-2. This has placed a strain on global sequencing capacity, especially in areas lacking the resources for large scale sequencing activities. Here we have developed three separate multiplex high-resolution melting assays to enable the identification of Alpha, Beta, Delta and Omicron VOCs. The assays were evaluated against whole genome sequencing on upper-respiratory swab samples collected during the Alpha, Delta and Omicron [BA.1] waves of the UK pandemic. The sensitivities of the eight individual primer sets were all 100%, and specificity ranged from 94.6 to 100%. The multiplex HRM assays have potential as a tool for high throughput surveillance of SARS-CoV-2 VOCs, particularly in areas with limited genomics facilities.
Collapse
|
17
|
Tosta S, Moreno K, Schuab G, Fonseca V, Segovia FMC, Kashima S, Elias MC, Sampaio SC, Ciccozzi M, Alcantara LCJ, Slavov SN, Lourenço J, Cella E, Giovanetti M. Global SARS-CoV-2 genomic surveillance: What we have learned (so far). INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105405. [PMID: 36681102 PMCID: PMC9847326 DOI: 10.1016/j.meegid.2023.105405] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/20/2023]
Abstract
The COVID-19 pandemic has brought significant challenges for genomic surveillance strategies in public health systems worldwide. During the past thirty-four months, many countries faced several epidemic waves of SARS-CoV-2 infections, driven mainly by the emergence and spread of novel variants. In that line, genomic surveillance has been a crucial toolkit to study the real-time SARS-CoV-2 evolution, for the assessment and optimization of novel diagnostic assays, and to improve the efficacy of existing vaccines. During the pandemic, the identification of emerging lineages carrying lineage-specific mutations (particularly those in the Receptor Binding domain) showed how these mutations might significantly impact viral transmissibility, protection from reinfection and vaccination. So far, an unprecedented number of SARS-CoV-2 viral genomes has been released in public databases (i.e., GISAID, and NCBI), achieving 14 million genome sequences available as of early-November 2022. In the present review, we summarise the global landscape of SARS-CoV-2 during the first thirty-four months of viral circulation and evolution. It demonstrates the urgency and importance of sustained investment in genomic surveillance strategies to timely identify the emergence of any potential viral pathogen or associated variants, which in turn is key to epidemic and pandemic preparedness.
Collapse
Affiliation(s)
- Stephane Tosta
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Keldenn Moreno
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Gabriel Schuab
- Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil.
| | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil
| | | | | | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | - Luiz Carlos Junior Alcantara
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo,Brazil; Butantan Institute, São Paulo, Brazil
| | - José Lourenço
- BioISI (Biosystems and Integrative Sciences Institute), Faculdade de Ciências da Universidade de Lisboa, Lisboa,Portugal
| | - Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA.
| | - Marta Giovanetti
- Interunit Postgraduate Program in Bioinformatics, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivirus, Instituto Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil; Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.
| |
Collapse
|
18
|
Kumar K, Tan WS, Arshad SS, Ho KL. Virus-like Particles of Nodavirus Displaying the Receptor Binding Domain of SARS-CoV-2 Spike Protein: A Potential VLP-Based COVID-19 Vaccine. Int J Mol Sci 2023; 24:ijms24054398. [PMID: 36901827 PMCID: PMC10001971 DOI: 10.3390/ijms24054398] [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: 12/03/2022] [Revised: 02/06/2023] [Accepted: 02/19/2023] [Indexed: 02/25/2023] Open
Abstract
Since the outbreak of the coronavirus disease 2019 (COVID-19), various vaccines have been developed for emergency use. The efficacy of the initial vaccines based on the ancestral strain of severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) has become a point of contention due to the emergence of new variants of concern (VOCs). Therefore, continuous innovation of new vaccines is required to target upcoming VOCs. The receptor binding domain (RBD) of the virus spike (S) glycoprotein has been extensively used in vaccine development due to its role in host cell attachment and penetration. In this study, the RBDs of the Beta (β) and Delta (δ) variants were fused to the truncated Macrobrachium rosenbergii nodavirus capsid protein without the protruding domain (CΔ116-MrNV-CP). Immunization of BALB/c mice with the virus-like particles (VLPs) self-assembled from the recombinant CP showed that, with AddaVax as an adjuvant, a significantly high level of humoral response was elicited. Specifically, mice injected with equimolar of adjuvanted CΔ116-MrNV-CP fused with the RBD of the β- and δ-variants increased T helper (Th) cell production with a CD8+/CD4+ ratio of 0.42. This formulation also induced proliferation of macrophages and lymphocytes. Overall, this study demonstrated that the nodavirus truncated CP fused with the SARS-CoV-2 RBD has potential to be developed as a VLP-based COVID-19 vaccine.
Collapse
Affiliation(s)
- Kiven Kumar
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Wen Siang Tan
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Siti Suri Arshad
- Department of Veterinary Pathology and Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
| | - Kok Lian Ho
- Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +603-9769-2729
| |
Collapse
|
19
|
Escudero-Pérez B, Lalande A, Mathieu C, Lawrence P. Host–Pathogen Interactions Influencing Zoonotic Spillover Potential and Transmission in Humans. Viruses 2023; 15:v15030599. [PMID: 36992308 PMCID: PMC10060007 DOI: 10.3390/v15030599] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/20/2023] [Indexed: 02/24/2023] Open
Abstract
Emerging infectious diseases of zoonotic origin are an ever-increasing public health risk and economic burden. The factors that determine if and when an animal virus is able to spill over into the human population with sufficient success to achieve ongoing transmission in humans are complex and dynamic. We are currently unable to fully predict which pathogens may appear in humans, where and with what impact. In this review, we highlight current knowledge of the key host–pathogen interactions known to influence zoonotic spillover potential and transmission in humans, with a particular focus on two important human viruses of zoonotic origin, the Nipah virus and the Ebola virus. Namely, key factors determining spillover potential include cellular and tissue tropism, as well as the virulence and pathogenic characteristics of the pathogen and the capacity of the pathogen to adapt and evolve within a novel host environment. We also detail our emerging understanding of the importance of steric hindrance of host cell factors by viral proteins using a “flytrap”-type mechanism of protein amyloidogenesis that could be crucial in developing future antiviral therapies against emerging pathogens. Finally, we discuss strategies to prepare for and to reduce the frequency of zoonotic spillover occurrences in order to minimize the risk of new outbreaks.
Collapse
Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, 20359 Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, 38124 Braunschweig, Germany
| | - Alexandre Lalande
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Cyrille Mathieu
- CIRI (Centre International de Recherche en Infectiologie), Team Neuro-Invasion, TROpism and VIRal Encephalitis, INSERM U1111, CNRS UMR5308, Université Claude Bernard Lyon 1, Ecole Normale Supérieure de Lyon, 69007 Lyon, France
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), 69002 Lyon, France
- Correspondence:
| |
Collapse
|
20
|
Shimada N, Shinoda M, Takei H, Yoshida Y, Nishimura M, Kousaka M, Morikawa M, Sato T, Matsuse H, Shinkai M. A case of reinfection with a different variant of SARS-CoV-2: case report. THE EGYPTIAN JOURNAL OF INTERNAL MEDICINE 2023; 35:13. [PMID: 36785595 PMCID: PMC9907179 DOI: 10.1186/s43162-023-00194-4] [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: 09/28/2022] [Accepted: 01/24/2023] [Indexed: 02/11/2023] Open
Abstract
Background Coronavirus disease 2019 (COVID-19) was previously thought to have a low reinfection rate, but there are concerns that the reinfection rate will increase with the emergence and spread of mutant variants. This report describes the case of a 36-year-old, non-immunosuppressed man who was infected twice by two different variants of COVID-19 within a relatively short period. Case presentation A 36-year-old Japanese man with no comorbidities was infected with the E484K variant (R.1 lineage) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Symptoms were mild and improved with symptomatic treatment alone. About four months later he presented to another outpatient department with high fever and headache. We diagnosed him as infected with the Alpha variant (B.1.1.7) of SARS-CoV-2 based on SARS-CoV-2 real-time reverse transcription polymerase chain reaction testing (RT-PCR). The patient was hospitalized with high fever. The patient received treatment in the form of anti-inflammatory therapy with corticosteroid and antibacterial chemotherapy. The patient improved without developing severe disease. Conclusion Concerns have been raised that the reinfection rate of COVID-19 will increase with the emergence of mutant variants. Particularly in mild cases, adequate amounts of neutralizing antibodies may not be produced, and reinfection may thus occur. Continued attention to sufficient infection control is thus essential.
Collapse
Affiliation(s)
- Nagashige Shimada
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masahiro Shinoda
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroaki Takei
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Yuto Yoshida
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan ,grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masashi Nishimura
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Mio Kousaka
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Miwa Morikawa
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Takashi Sato
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| | - Hiroto Matsuse
- grid.470115.6Division of Respiratory Medicine, Department of Internal Medicine, Toho University Ohashi Medical Center, Tokyo, Japan
| | - Masaharu Shinkai
- Department of Respiratory Medicine, Tokyo Shinagawa Hospital, Tokyo, Japan
| |
Collapse
|
21
|
Zhou B, Zhou H, Zhang X, Xu X, Chai Y, Zheng Z, Kot AC, Zhou Z. TEMPO: A transformer-based mutation prediction framework for SARS-CoV-2 evolution. Comput Biol Med 2023; 152:106264. [PMID: 36535209 PMCID: PMC9747230 DOI: 10.1016/j.compbiomed.2022.106264] [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: 09/18/2022] [Revised: 10/16/2022] [Accepted: 10/30/2022] [Indexed: 12/15/2022]
Abstract
The widespread of SARS-CoV-2 presents a significant threat to human society, as well as public health and economic development. Extensive efforts have been undertaken to battle against the pandemic, whereas effective approaches such as vaccination would be weakened by the continuous mutations, leading to considerable attention being attracted to the mutation prediction. However, most previous studies lack attention to phylogenetics. In this paper, we propose a novel and effective model TEMPO for predicting the mutation of SARS-CoV-2 evolution. Specifically, we design a phylogenetic tree-based sampling method to generate sequence evolution data. Then, a transformer-based model is presented for the site mutation prediction after learning the high-level representation of these sequence data. We conduct experiments to verify the effectiveness of TEMPO, leveraging a large-scale SARS-CoV- 2 dataset. Experimental results show that TEMPO is effective for mutation prediction of SARS- CoV-2 evolution and outperforms several state-of-the-art baseline methods. We further perform mutation prediction experiments of other infectious viruses, to explore the feasibility and robustness of TEMPO, and experimental results verify its superiority. The codes and datasets are freely available at https://github.com/ZJUDataIntelligence/TEMPO.
Collapse
Affiliation(s)
- Binbin Zhou
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; Industry Brain Institute, Zhejiang University City College, Hangzhou, 310015, China.
| | - Hang Zhou
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; College of Computer Science and Technology, Zhejiang University, Hangzhou, 310027, China.
| | - Xue Zhang
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Xiaobin Xu
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China.
| | - Yi Chai
- ZJU-UoE Institute, Zhejiang University, Haining, 314400, China.
| | - Zengwei Zheng
- Department of Computer Science and Computing, Zhejiang University City College, No. 48 Huzhou Street, Hangzhou, 310015, China; Industry Brain Institute, Zhejiang University City College, Hangzhou, 310015, China.
| | - Alex Chichung Kot
- School of Electrical and Electronic Engineering, Nanyang Technological University, 639798, Singapore.
| | - Zhan Zhou
- Innovation Institute for Artificial Intelligence in Medicine and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, 310058, China; The Fourth Affiliated Hospital, Zhejiang University School of Medicine, Yiwu, 322000, China; Alibaba-Zhejiang University Joint Research Center of Future Digital Healthcare, Hangzhou, 310058, China.
| |
Collapse
|
22
|
Taus E, Hofmann C, Ibarrondo FJ, Gong LS, Hausner MA, Fulcher JA, Krogstad P, Kitchen SG, Ferbas KG, Tobin NH, Rimoin AW, Aldrovandi GM, Yang OO. Persistent memory despite rapid contraction of circulating T Cell responses to SARS-CoV-2 mRNA vaccination. Front Immunol 2023; 14:1100594. [PMID: 36860850 PMCID: PMC9968837 DOI: 10.3389/fimmu.2023.1100594] [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: 11/17/2022] [Accepted: 01/24/2023] [Indexed: 02/17/2023] Open
Abstract
Introduction While antibodies raised by SARS-CoV-2 mRNA vaccines have had compromised efficacy to prevent breakthrough infections due to both limited durability and spike sequence variation, the vaccines have remained highly protective against severe illness. This protection is mediated through cellular immunity, particularly CD8+ T cells, and lasts at least a few months. Although several studies have documented rapidly waning levels of vaccine-elicited antibodies, the kinetics of T cell responses have not been well defined. Methods Interferon (IFN)-γ enzyme-linked immunosorbent spot (ELISpot) assay and intracellular cytokine staining (ICS) were utilized to assess cellular immune responses (in isolated CD8+ T cells or whole peripheral blood mononuclear cells, PBMCs) to pooled peptides spanning spike. ELISA was performed to quantitate serum antibodies against the spike receptor binding domain (RBD). Results In two persons receiving primary vaccination, tightly serially evaluated frequencies of anti-spike CD8+ T cells using ELISpot assays revealed strikingly short-lived responses, peaking after about 10 days and becoming undetectable by about 20 days after each dose. This pattern was also observed in cross-sectional analyses of persons after the first and second doses during primary vaccination with mRNA vaccines. In contrast, cross-sectional analysis of COVID-19-recovered persons using the same assay showed persisting responses in most persons through 45 days after symptom onset. Cross-sectional analysis using IFN-γ ICS of PBMCs from persons 13 to 235 days after mRNA vaccination also demonstrated undetectable CD8+ T cells against spike soon after vaccination, and extended the observation to include CD4+ T cells. However, ICS analyses of the same PBMCs after culturing with the mRNA-1273 vaccine in vitro showed CD4+ and CD8+ T cell responses that were readily detectable in most persons out to 235 days after vaccination. Discussion Overall, we find that detection of spike-targeted responses from mRNA vaccines using typical IFN-γ assays is remarkably transient, which may be a function of the mRNA vaccine platform and an intrinsic property of the spike protein as an immune target. However, robust memory, as demonstrated by capacity for rapid expansion of T cells responding to spike, is maintained at least several months after vaccination. This is consistent with the clinical observation of vaccine protection from severe illness lasting months. The level of such memory responsiveness required for clinical protection remains to be defined.
Collapse
Affiliation(s)
- Ellie Taus
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Christian Hofmann
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - F Javier Ibarrondo
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Laura S Gong
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Mary Ann Hausner
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Jennifer A Fulcher
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Paul Krogstad
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Scott G Kitchen
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Kathie G Ferbas
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Nicole H Tobin
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Anne W Rimoin
- Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, United States
| | - Grace M Aldrovandi
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| | - Otto O Yang
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States.,Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States
| |
Collapse
|
23
|
Huang L, Lai FTT, Yan VKC, Cheng FWT, Cheung CL, Chui CSL, Li X, Wan EYF, Wong CKH, Hung IFN, Lau CS, Wong ICK, Chan EWY. Comparing hybrid and regular COVID-19 vaccine-induced immunity against the Omicron epidemic. NPJ Vaccines 2022; 7:162. [PMCID: PMC9753877 DOI: 10.1038/s41541-022-00594-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/06/2022] [Indexed: 12/16/2022] Open
Abstract
AbstractEvidence on the effectiveness of COVID-19 vaccines among people who recovered from a previous SARS-CoV-2 infection is warranted to inform vaccination recommendations. Using the territory-wide public healthcare and vaccination records of over 2.5 million individuals in Hong Kong, we examined the potentially differential risk of SARS-CoV-2 infection, hospitalization, and mortality between those receiving two homologous doses of BNT162b2 or CoronaVac versus those with a previous infection receiving only one dose amid the Omicron epidemic. Results show a single dose after a SARS-CoV-2 infection is associated with a lower risk of infection (BNT162b2: adjusted incidence rate ratio [IRR] = 0.475, 95% CI: 0.410–0.550; CoronaVac: adjusted IRR = 0.397, 95% CI: 0.309–0.511) and no significant difference was detected in the risk of COVID-19-related hospitalization or mortality compared with a two-dose vaccination regimen. Findings support clinical recommendations that those with a previous infection could receive a single dose to gain at least similar protection as those who received two doses without a previous infection.
Collapse
|
24
|
SARS-CoV-2 Genomic Surveillance in Brazil: A Systematic Review with Scientometric Analysis. Viruses 2022; 14:v14122715. [PMID: 36560720 PMCID: PMC9784312 DOI: 10.3390/v14122715] [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: 09/20/2022] [Revised: 11/30/2022] [Accepted: 12/02/2022] [Indexed: 12/09/2022] Open
Abstract
Several studies have monitored the SARS-CoV-2 variants in Brazil throughout the pandemic. Here, we systematically reviewed and conducted a scientometric analysis of the SARS-CoV-2 genomic surveillance studies using Brazilian samples. A Pubmed database search on October 2022 returned 492 articles, of which 106 were included. Ninety-six different strains were reported, with variant of concern (VOC) gamma (n = 35,398), VOC delta (n = 15,780), and the variant of interest zeta (n = 1983) being the most common. The top three states with the most samples in the published articles were São Paulo, Rio de Janeiro, and Minas Gerais. Whereas the first year of the pandemic presented primary circulation of B.1.1.28 and B.1.1.33 variants, consecutive replacements were observed between them and VOI zeta, VOC gamma, VOC delta, and VOC omicron. VOI mu, VOI lambda, VOC alpha, and VOC beta were also detected but failed to reach significant circulation. Co-infection, re-infection, and vaccine breakthrough reports were found. Article co-citation differed from the co-authorship structure. Despite the limitations, we expect to give an overview of Brazil's genomic surveillance studies and contribute to future research execution.
Collapse
|
25
|
Lim HT, Kok BH, Lim CP, Abdul Majeed AB, Leow CY, Leow CH. Single domain antibodies derived from ancient animals as broadly neutralizing agents for SARS-CoV-2 and other coronaviruses. BIOMEDICAL ENGINEERING ADVANCES 2022; 4:100054. [PMID: 36158162 PMCID: PMC9482557 DOI: 10.1016/j.bea.2022.100054] [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: 07/03/2022] [Revised: 09/06/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022] Open
Abstract
With severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as an emergent human virus since December 2019, the world population is susceptible to coronavirus disease 2019 (COVID-19). SARS-CoV-2 has higher transmissibility than the previous coronaviruses, associated by the ribonucleic acid (RNA) virus nature with high mutation rate, caused SARS-CoV-2 variants to arise while circulating worldwide. Neutralizing antibodies are identified as immediate and direct-acting therapeutic against COVID-19. Single-domain antibodies (sdAbs), as small biomolecules with non-complex structure and intrinsic stability, can acquire antigen-binding capabilities comparable to conventional antibodies, which serve as an attractive neutralizing solution. SARS-CoV-2 spike protein attaches to human angiotensin-converting enzyme 2 (ACE2) receptor on lung epithelial cells to initiate viral infection, serves as potential therapeutic target. sdAbs have shown broad neutralization towards SARS-CoV-2 with various mutations, effectively stop and prevent infection while efficiently block mutational escape. In addition, sdAbs can be developed into multivalent antibodies or inhaled biotherapeutics against COVID-19.
Collapse
Affiliation(s)
- H T Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - B H Kok
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - C P Lim
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - A B Abdul Majeed
- Faculty of Pharmacy, Universiti Teknologi MARA, Kampus Puncak Alam, Bandar Puncak Alam, Selangor 42300, Malaysia
| | - C Y Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| | - C H Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Gelugor, Penang 11800, Malaysia
| |
Collapse
|
26
|
Halfmann PJ, Minor NR, Haddock III LA, Maddox R, Moreno GK, Braun KM, Baker DA, Riemersa KK, Prasad A, Alman KJ, Lambert MC, Florek K, Bateman A, Westergaard R, Safdar N, Andes DR, Kawaoka Y, Fida M, Yao JD, Friedrich TC, O’Connor DH. Evolution of a globally unique SARS-CoV-2 Spike E484T monoclonal antibody escape mutation in a persistently infected, immunocompromised individual. Virus Evol 2022; 9:veac104. [PMID: 37692895 PMCID: PMC10491860 DOI: 10.1093/ve/veac104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/29/2022] [Accepted: 11/04/2022] [Indexed: 09/12/2023] Open
Abstract
Prolonged infections in immunocompromised individuals may be a source for novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variants, particularly when both the immune system and antiviral therapy fail to clear the infection and enable within-host evolution. Here we describe a 486-day case of SARS-CoV-2 infection in an immunocompromised individual. Following monotherapy with the monoclonal antibody Bamlanivimab, the individual's virus acquired resistance, likely via the earliest known occurrence of Spike amino acid variant E484T. Recently, E484T has arisen again as a derivative of E484A in the Omicron Variant of Concern, supporting the hypothesis that prolonged infections can give rise to novel variants long before they become prevalent in the human population.
Collapse
Affiliation(s)
- Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Nicholas R Minor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Luis A Haddock III
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Robert Maddox
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Gage K Moreno
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Katarina M Braun
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David A Baker
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kasen K Riemersa
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Ankur Prasad
- Division of Allergy, Pulmonary and Critical Care Medicine, School of Medicine and Public Health, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705-2281, USA
| | - Kirsten J Alman
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Matthew C Lambert
- University of Wisconsin Division of Infectious Disease, Room 5275-07C, 1685 Highland Avenue, Madison, WI 53705, USA
| | - Kelsey Florek
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Allen Bateman
- Wisconsin State Laboratory of Hygiene, 2601 Agriculture Drive, PO Box 7996, Madison, WI 53707, USA
| | - Ryan Westergaard
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Nasia Safdar
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - David R Andes
- Department of Medicine, 1685 Highland Avenue, 5158 Medical Foundation Centennial Building, Madison, WI 53705, USA
| | - Yoshihiro Kawaoka
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - Madiha Fida
- Division of Infectious Diseases, Mayo Clinic, 200 First St. SW, Rochester, Rochester, Minnesota 55905, USA
| | - Joseph D Yao
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, 2015 Linden Dr, Madison, WI 53706, USA
| | - David H O’Connor
- Department of Pathology and Laboratory Medicine, 3170 UW Medical Foundation Centennial Building (MFCB), 1685 Highland Avenue, Madison, WI 53705, USA
| |
Collapse
|
27
|
García JE, González-López VA, Tasca GH. Multiple partition Markov model for B.1.1.7, B.1.351, B.1.617.2, and P.1 variants of SARS-CoV 2 virus. Comput Stat 2022:1-37. [PMID: 36338539 PMCID: PMC9628379 DOI: 10.1007/s00180-022-01291-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 09/27/2022] [Indexed: 11/25/2022]
Abstract
With tools originating from Markov processes, we investigate the similarities and differences between genomic sequences in FASTA format coming from four variants of the SARS-CoV 2 virus, B.1.1.7 (UK), B.1.351 (South Africa), B.1.617.2 (India), and P.1 (Brazil). We treat the virus' sequences as samples of finite memory Markov processes acting in A = { a , c , g , t } . We model each sequence, revealing some heterogeneity between sequences belonging to the same variant. We identified the five most representative sequences for each variant using a robust notion of classification, see Fernández et al. (Math Methods Appl Sci 43(13):7537-7549. 10.1002/mma.5705 ). Using a notion derived from a metric between processes, see García et al. (Appl Stoch Models Bus Ind 34(6):868-878. 10.1002/asmb.2346), we identify four groups, each group representing a variant. It is also detected, by this metric, global proximity between the variants B.1.351 and B.1.1.7. With the selected sequences, we assemble a multiple partition model, see Cordeiro et al. (Math Methods Appl Sci 43(13):7677-7691. 10.1002/mma.6079), revealing in which states of the state space the variants differ, concerning the mechanisms for choosing the next element in A. Through this model, we identify that the variants differ in their transition probabilities in eleven states out of a total of 256 states. For these eleven states, we reveal how the transition probabilities change from variant (group of variants) to variant (group of variants). In other words, we indicate precisely the stochastic reasons for the discrepancies.
Collapse
Affiliation(s)
- Jesús Enrique García
- Department of Statistics, University of Campinas, Sergio Buarque de Holanda, 651, Campinas, São Paulo, CEP: 13083-859 Brazil
| | - Verónica Andrea González-López
- Department of Statistics, University of Campinas, Sergio Buarque de Holanda, 651, Campinas, São Paulo, CEP: 13083-859 Brazil
| | | |
Collapse
|
28
|
Retrospective Analysis of the SARS-CoV-2 Infection Profile in COVID-19 Positive Patients in Vitoria da Conquista, Northeast Brazil. Viruses 2022; 14:v14112424. [PMID: 36366521 PMCID: PMC9699198 DOI: 10.3390/v14112424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is responsible for causing Coronavirus Disease-2019 (COVID-19), a heterogeneous clinical condition that manifests varying symptom severity according to the demographic profile of the studied population. While many studies have focused on the spread of COVID-19 in large urban centers in Brazil, few have evaluated medium or small cities in the Northeast region. The aims of this study were: (i) to identify risk factors for mortality from SARS-CoV-2 infection, (ii) to evaluate the gene expression patterns of key immune response pathways using nasopharyngeal swabs of COVID-19 patients, and (iii) to identify the circulating SARS-CoV-2 variants in the residents of a medium-sized city in Northeast Brazil. A total of 783 patients infected with SARS-CoV-2 between May 2020 and August 2021 were included in this study. Clinical-epidemiological data from patients who died and those who survived were compared. Patients were also retrospectively divided into three groups based on disease severity: asymptomatic, mild, and moderate/severe. Samples were added to a qPCR array for analyses of 84 genes involved with immune response pathways and sequenced using the Oxford Nanopore MinION technology. Having pre-existing comorbidity; being male; having cardiovascular disease, diabetes, and/or chronic obstructive pulmonary disease; and PCR cycle threshold (Ct) values under 22 were identified as risk factors for mortality. Analysis of the expression profiles of inflammatory pathway genes showed that the greater the infection severity, the greater the activation of inflammatory pathways, triggering the cytokine storm and downregulating anti-inflammatory pathways. Viral genome analysis revealed the circulation of multiple lineages, such as B.1, B.1.1.28, Alpha, and Gamma, suggesting that multiple introduction events had occurred over time. This study's findings help identify the specific strains and increase our understanding of the true state of local health. In addition, our data demonstrate that epidemiological and genomic surveillance together can help formulate public health strategies to guide governmental actions.
Collapse
|
29
|
Marinov GK, Mladenov M, Rangachev A, Alexiev I. SARS-CoV-2 reinfections during the first three major COVID-19 waves in Bulgaria. PLoS One 2022; 17:e0274509. [PMID: 36084070 PMCID: PMC9462809 DOI: 10.1371/journal.pone.0274509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/30/2022] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a devastating impact on the world over the past two years (2020-2021). One of the key questions about its future trajectory is the protection from subsequent infections and disease conferred by a previous infection, as the SARS-CoV-2 virus belongs to the coronaviruses, a group of viruses the members of which are known for their ability to reinfect convalescent individuals. Bulgaria, with high rates of previous infections combined with low vaccination rates and an elderly population, presents a somewhat unique context to study this question. METHODS We use detailed governmental data on registered COVID-19 cases to evaluate the incidence and outcomes of COVID-19 reinfections in Bulgaria in the period between March 2020 and early December 2021. RESULTS For the period analyzed, a total of 4,106 cases of individuals infected more than once were observed, including 31 cases of three infections and one of four infections. The number of reinfections increased dramatically during the Delta variant-driven wave of the pandemic towards the end of 2021. We observe a moderate reduction of severe outcomes (hospitalization and death) in reinfections relative to primary infections, and a more substantial reduction of severe outcomes in breakthrough infections in vaccinated individuals. CONCLUSIONS In the available datasets from Bulgaria, prior infection appears to provide some protection from severe outcomes, but to a lower degree than the reduction in severity of breakthrough infections in the vaccinated compared to primary infections in the unvaccinated.
Collapse
Affiliation(s)
- Georgi K. Marinov
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | | | - Antoni Rangachev
- Institute of Mathematics and Informatics, Bulgarian Academy of Sciences, Sofia, Bulgaria
- International Center for Mathematical Sciences-Sofia, Sofia, Bulgaria
| | - Ivailo Alexiev
- National Center of Infectious and Parasitic Diseases, Sofia, Bulgaria
| |
Collapse
|
30
|
Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
Collapse
Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
| |
Collapse
|
31
|
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San EJ, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, Iani FCDM, de Carvalho Pereira G, Vazquez C, Sanabria GME, Oliveira ECD, Demarchi L, Croda J, Dos Santos Bezerra R, Paola Oliveira de Lima L, Martins AJ, Renata Dos Santos Barros C, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, Reboredo de Oliveira da Silva L, Gómez MKA, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Barbosa Da Silva L, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Figueredo GPM, Fava WS, Motta-Castro ARC, Venturini J, do Vale Leone de Oliveira SM, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Giacomini MP, Marques NQ, Riediger IN, Raboni S, Mattoso G, Cataneo AD, Zanluca C, Duarte Dos Santos CN, Assato PA, Allan da Silva da Costa F, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, Bispo de Filippis AM, Venancio da Cunha R, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, Navegantes W, do Carmo Said RF, Campelo de A E Melo CF, Almiron M, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, Junior de Alcantara LC, Covas DT. Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil. Nat Microbiol 2022; 7:1490-1500. [PMID: 35982313 PMCID: PMC9417986 DOI: 10.1038/s41564-022-01191-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 06/28/2022] [Indexed: 01/01/2023]
Abstract
The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy
| | - Svetoslav Nanev Slavov
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
- Butantan Institute, São Paulo, Brazil
| | - Vagner Fonseca
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Houriiyah Tegally
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | | | - Emmanuel James San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Evandra Strazza Rodrigues
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Elaine Vieira Santos
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Flavia Aburjaile
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felicidade Pereira
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Arabela Leal
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Glauco de Carvalho Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gladys Mercedes Estigarribia Sanabria
- Laboratório Central de Salud Pública, Asunción, Paraguay
- Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay
- Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | | | - Luiz Demarchi
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul (LACEN-MS), Campo Grande, Mato Grosso do Sul, Brazil
| | - Julio Croda
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Rafael Dos Santos Bezerra
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Vlademir Vicente Cantarelli
- Universidade Federal de Ciencias da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Vanessa Brandão Nardy
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | | | | | - Jaqueline Gomes Lima
- Laboratório Central de Saúde Pública do Estado da Bahia (LACEN-BA), Salvador, Bahia, Brazil
| | - Adriana Aparecida Ribeiro
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natália Rocha Guimarães
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Takao Watanabe
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | - Luana Barbosa Da Silva
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | - Raquel da Silva Ferreira
- Laboratório Central de Saúde Pública do Estado de Mato Grosso (LACEN-MT), Cuiabá, Mato Grosso, Brazil
| | | | | | | | | | - Juan Torales
- Laboratório Central de Salud Pública, Asunción, Paraguay
| | | | | | - Gloria Patricia Martínez Figueredo
- Laboratório Central de Salud Pública, Asunción, Paraguay
- Instituto Regional de Investigación em Salud, Universidad Nacional del Caaguazú, Caaguazú, Paraguay
- Laboratório de Biología Molecular, Hospital Regional de Coronel Oviedo, Ministerio de Salud Pública y Bienestar Social, Asunción, Paraguay
| | | | | | - James Venturini
- Universidade Federal do Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | | | | | - Guilherme Nardi Becker
- Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil
| | | | - Nelson Quallio Marques
- Laboratório Central de Saúde Pública do Estado do Paraná (Lacen-PR), Curitiba, Paraná, Brazil
| | | | - Sonia Raboni
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Gabriela Mattoso
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Allan D Cataneo
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | - Camila Zanluca
- Laboratório de Virologia Molecular, Instituto Carlos Chagas/Fiocruz-PR, Curitiba, Paraná, Brazil
| | | | - Patricia Akemi Assato
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Felipe Allan da Silva da Costa
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Cecilia Artico Banho
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Lívia Sacchetto
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Marília Mazzi Moraes
- Medicine School of São José do Rio Preto (FAMERP), São José do Rio Preto, São Paulo, Brazil
| | - Rejane Maria Tommasini Grotto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, São Paulo, Brazil
| | - Jayme A Souza-Neto
- Department of Bioprocesses and Biotechnology, School of Agricultural Sciences, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil
| | | | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- Centro de Genômica Funcional da ESALQ, University of São Paulo, Piracicaba, São Paulo, Brazil
| | - Rodrigo Tocantins Calado
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | | | | | | | - Carla Freitas
- Coordenação Geral dos Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde, (CGLAB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cássia de Fátima Rangel Fernandes
- Departamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilancia em Saude, Ministerio da Saude, Brasılia, Distrito Federal, Brazil
| | - Wildo Navegantes
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
| | | | | | - Maria Almiron
- Pan American Health Organization (PAHO)/World Health Organization (WHO), Brasilia, Distrito Federal, Brazil
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, UK
- Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Laboratório Central de Saúde Pública do Estado de Minas Gerais (LACEN-MG), Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, New South Wales, Australia
| | | | | | | | - Simone Kashima
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
| | - Luiz Carlos Junior de Alcantara
- Laboratório de Flavivirus, Fundacao Oswaldo Cruz, Rio de Janeiro, Brazil.
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.
| | - Dimas Tadeu Covas
- Blood Center of Ribeirão Preto, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
- Butantan Institute, São Paulo, Brazil.
| |
Collapse
|
32
|
Samara AA, Boutlas S, Janho MB, Gourgoulianis KI, Sotiriou S. COVID-19 Severity and Mortality after Vaccination against SARS-CoV-2 in Central Greece. J Pers Med 2022; 12:jpm12091423. [PMID: 36143207 PMCID: PMC9502864 DOI: 10.3390/jpm12091423] [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: 07/12/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 11/29/2022] Open
Abstract
Background: Vaccination against SARS-CoV-2 (COVID-19) has become crucial for limiting disease transmission and reducing its severity, hospitalizations and mortality; however, despite universal acceptance, vaccine hesitancy is still significant. In the present manuscript, we aim to assess COVID-19-attributed mortality after the prevalence of new variants of the virus (Delta and Omicron viral strains) and to evaluate the vaccination effect. Methods: All patients that were hospitalized due to COVID-19 infection in the Respiratory Department of a tertiary referral center in central Greece between 1st of June 2021 and 1st of February 2022 were included in the present study. Results: 760 consecutive patients were included in the study; 89 (11.7%) were diagnosed with severe COVID-19 and 220 (38.7%) patients were fully vaccinated. In logistic regression, increased age (aOR = 1.12, p < 0.001), male gender (aOR = 2.29, p = 0.013) and vaccination against SARS-CoV-2 virus (aOR = 0.2, p < 0.001) were associated with mortality attributed to COVID-19 with a statistically significant association. Moreover, increased age (aOR = 1.09, p < 0.001), male gender (aOR = 1.92, p = 0.025) and vaccination against SARS-CoV-2 virus (aOR = 0.25, p < 0.001) were statistically significantly associated with clinical severity of COVID-19 infection. However, when comparing the length of hospitalization between vaccinated and unvaccinated patients, the difference was not statistically significant between the two groups (p = 0.138). Conclusions: Vaccination against SARS-CoV-2 virus had a protective effect in terms of mortality and clinical severity of COVID-19 during the fourth wave of the pandemic in Central Greece. The national vaccination policy has to focus on vulnerable populations that are expected to benefit the most from the vaccine’s protection.
Collapse
Affiliation(s)
- Athina A. Samara
- Department of Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
- Correspondence: ; Tel.: +30-241-350-1701
| | - Stylianos Boutlas
- Department of Respiratory Medicine, Faculty of Medicine, University of Thessaly, 41110 Larissa, Greece
| | - Michel B. Janho
- Department of Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| | | | - Sotirios Sotiriou
- Department of Embryology, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece
| |
Collapse
|
33
|
Ao Z, Ouyang MJ, Olukitibi TA, Yao X. SARS-CoV-2 Delta spike protein enhances the viral fusogenicity and inflammatory cytokine production. iScience 2022; 25:104759. [PMID: 35854977 PMCID: PMC9281453 DOI: 10.1016/j.isci.2022.104759] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 04/14/2022] [Accepted: 07/11/2022] [Indexed: 12/24/2022] Open
Abstract
The Delta variant had spread globally in 2021 and caused more serious disease than the original virus and Omicron variant. In this study, we investigated several virological features of Delta spike protein (SPDelta), including protein maturation, its impact on viral entry of pseudovirus and cell-cell fusion, and its induction of inflammatory cytokine production in human macrophages and dendritic cells. The results showed that SPΔCDelta exhibited enhanced S1/S2 cleavage in cells and pseudotyped virus-like particles (PVLPs). Further, SPΔCDelta elevated pseudovirus entry in human lung cell lines and significantly enhanced syncytia formation. Furthermore, we revealed that SPΔCDelta-PVLPs had stronger effects on stimulating NF-κB and AP-1 signaling in human monocytic THP1 cells and induced significantly higher levels of proinflammatory cytokine, such as TNF-α, IL-1β, and IL-6, released from human macrophages and dendritic cells. Overall, these studies provide evidence to support the important role of SPΔCDelta during virus infection, transmission, and pathogenesis.
Collapse
Affiliation(s)
- Zhujun Ao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Maggie Jing Ouyang
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Titus Abiola Olukitibi
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Xiaojian Yao
- Laboratory of Molecular Human Retrovirology, Department of Medical Microbiology, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| |
Collapse
|
34
|
Tsuchiya K, Yamamoto N, Hosaka Y, Wakita M, Hiki M, Matsushita Y, Mori H, Hori S, Misawa S, Miida T, Nojiri S, Takahashi K, Naito T, Tabe Y. Molecular characterization of SARS-CoV-2 detected in Tokyo, Japan during five waves: Identification of the amino acid substitutions associated with transmissibility and severity. Front Microbiol 2022; 13:912061. [PMID: 35966679 PMCID: PMC9363898 DOI: 10.3389/fmicb.2022.912061] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Many variants of SARS-CoV-2 have emerged around the world. It is therefore important to understand its global viral evolution and the corresponding mutations associated with transmissibility and severity. In this study, we analyzed 112 whole genome sequences of SARS-CoV-2 collected from patients at Juntendo University Hospital in Tokyo and the genome data from entire Japan deposited in Global Initiative on Sharing Avian Influenza Data (GISAID) to examine the relationship of amino acid changes with the transmissibility and the severity of each strain/lineage. We identified 12 lineages, including B.1.1.284, B.1.1.214, R.1, AY.29, and AY.29.1, which were prevalent specifically in Japan. B.1.1.284 was most frequently detected in the second wave, but B.1.1.214 became the predominant lineage in the third wave, indicating that B.1.1.214 has a higher transmissibility than B.1.1.284. The most prevalent lineage during the fourth and fifth wave was B.1.1.7 and AY.29, respectively. In regard to the severity of identified lineages, B.1.1.214 was significantly lower than the reference lineage, B.1.1.284. Analysis of the genome sequence and other traits of each lineage/strain revealed the mutations in S, N, and NSPs that increase the transmissibility and/or severity. These mutations include S: M153T, N: P151L, NSP3: S543P, NSP5: P108S, and NSP12: A423V in B.1.1.284; S: W152L and E484K in R.1; S: H69del, V70del, and N501Y in the Alpha strain; S: L452R, T478K, and P681R in the Delta strain. Furthermore, it is suggested that the transmissibility of B.1.1.214 could be enhanced by the mutations N: M234I, NSP14: P43L, and NSP16: R287I. To address the issue of the virus evolution, it is necessary to continuously monitor the genomes of SARS-CoV-2 and analyze the effects of mutations for developing vaccines and antiviral drugs effective against SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Koji Tsuchiya
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo, Tokyo, Japan
| | - Norio Yamamoto
- Department of General Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
- Department of Microbiology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
- Department of Microbiology, Tokai University School of Medicine, Isehara, Japan
- *Correspondence: Norio Yamamoto, ;
| | - Yoshie Hosaka
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo, Tokyo, Japan
| | - Mitsuru Wakita
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo, Tokyo, Japan
| | - Makoto Hiki
- Department of Emergency Medicine, Juntendo University Faculty of Medicine, Bunkyo-ku, Japan
- Department of Cardiovascular Biology and Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Yasushi Matsushita
- Department of Internal Medicine and Rheumatology, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Hirotake Mori
- Department of General Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Satoshi Hori
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
- Department of Infection Control Science, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Shigeki Misawa
- Department of Clinical Laboratory, Juntendo University Hospital, Bunkyo, Tokyo, Japan
| | - Takashi Miida
- Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Bunkyo-ku, Japan
| | - Shuko Nojiri
- Medical Technology Innovation Center, Juntendo University, Bunkyo-ku, Japan
| | - Kazuhisa Takahashi
- Department of Respiratory Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Toshio Naito
- Department of General Medicine, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| | - Yoko Tabe
- Department of Clinical Laboratory Medicine, Juntendo University Faculty of Medicine, Bunkyo-ku, Japan
- Department of Research Support Utilizing Bioresource Bank, Juntendo University Graduate School of Medicine, Bunkyo-ku, Japan
| |
Collapse
|
35
|
Rosenberg M, Chen C, Golzarri-Arroyo L, Carroll A, Menachemi N, Ludema C. SARS-CoV-2 reinfections in a US university setting, Fall 2020 to Spring 2021. BMC Infect Dis 2022; 22:592. [PMID: 35787250 PMCID: PMC9252534 DOI: 10.1186/s12879-022-07578-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 06/23/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND SARS-CoV-2 reinfections are a public health concern because of the potential for transmission and clinical disease, and because of our limited understanding of whether and how well an infection confers protection against subsequent infections. Despite the public health importance, few studies have reported rigorous estimates of reinfection risk. METHODS Leveraging Indiana University's comprehensive testing program to identify both asymptomatic and symptomatic SARS-CoV-2 cases, we estimated the incidence of SARS-CoV-2 reinfection among students, faculty, and staff across the 2020-2021 academic year. We contextualized the reinfection data with information on key covariates: age, sex, Greek organization membership, student vs faculty/staff affiliation, and testing type. RESULTS Among 12,272 people with primary infections, we found a low level of SARS-CoV-2 reinfections (0.6%; 0.4 per 10,000 person-days). We observed higher risk for SARS-CoV-2 reinfections in Greek-affiliated students. CONCLUSIONS We found evidence for low levels of SARS-CoV-2 reinfection in a large multi-campus university population during a time-period prior to widespread COVID-19 vaccination.
Collapse
Affiliation(s)
- Molly Rosenberg
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, 1025 E. 7th St., Bloomington, IN, 47405, USA.
| | - Chen Chen
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, 1025 E. 7th St., Bloomington, IN, 47405, USA
| | - Lilian Golzarri-Arroyo
- Biostatistics Consulting Center, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA
| | - Aaron Carroll
- Pediatric and Adolescent Comparative Effectiveness Research, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Nir Menachemi
- Department of Health Policy and Management, Indiana University Fairbanks School of Public Health at IUPUI, Indianapolis, IN, USA
| | - Christina Ludema
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, 1025 E. 7th St., Bloomington, IN, 47405, USA
| |
Collapse
|
36
|
Eweas AF, Osman HEH, Naguib IA, Abourehab MAS, Abdel-Moneim AS. Virtual Screening of Repurposed Drugs as Potential Spike Protein Inhibitors of Different SARS-CoV-2 Variants: Molecular Docking Study. Curr Issues Mol Biol 2022; 44:3018-3029. [PMID: 35877432 PMCID: PMC9319331 DOI: 10.3390/cimb44070208] [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: 06/06/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/26/2022] Open
Abstract
Like most of the RNA viruses, SARS-CoV-2 continuously mutates. Although many mutations have an insignificant impact on the virus properties, mutations in the surface protein, especially those in the receptor-binding domain, may lead to immune or vaccine escape variants, or altered binding activities to both the cell receptor and the drugs targeting such a protein. The current study intended to assess the ability of different variants of interest (VOIs) and variants of concern (VOCs) of SARS-CoV-2 for their affinities of binding to different repurposed drugs. Seven FDA approved drugs, namely, camostat, nafamostat mesylate, fenofibrate, umifenovir, nelfinavir, cefoperazone and ceftazidime, were selected based on their reported in vitro and clinical activities against SARA-CoV-2. The S1 protein subunit from eleven different variants, including the latest highly contiguous omicron variant, were used as targets for the docking study. The docking results revealed that all tested drugs possess moderate to high binding energies to the receptor-binding domain (RBD) of the S1 protein for all different variants. Cefoperazone was found to possess the highest binding energy to the RBD of the S1 protein of all the eleven variants. Ceftazidime was the second-best drug in terms of binding affinity towards the S1 RBD of the investigated variants. On the other hand, fenofibrate showed the least binding affinity towards the RBD of the S1 protein of all eleven variants. The binding affinities of anti-spike drugs varied among different variants. Most of the interacting amino acid residues of the receptor fall within the RBD (438–506).
Collapse
Affiliation(s)
- Ahmad F. Eweas
- Department of Pharmaceutical and Medicinal Chemistry, National Research Centre, Cairo 12622, Egypt;
- Department of Science, University of Technology and Applied Sciences Rustaq, Rustaq 133, Oman
| | - Hosam-Eldin H. Osman
- Department of Anatomy, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Ibrahim A. Naguib
- Department of Pharmaceutical Chemistry, College of Pharmacy, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Mohammed A. S. Abourehab
- Department of Pharmaceutics, Faculty of Pharmacy, Umm Al-Qura University, Makkah 21955, Saudi Arabia;
- Department of Pharmaceutics, College of Pharmacy, Minia University, Minia 61519, Egypt
| | - Ahmed S. Abdel-Moneim
- Department of Microbiology, College of Medicine, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia
- Correspondence: or
| |
Collapse
|
37
|
Kato Y, Nishiyama K, Nishimura A, Noda T, Okabe K, Kusakabe T, Kanda Y, Nishida M. Drug repurposing for the treatment of COVID-19. J Pharmacol Sci 2022; 149:108-114. [PMID: 35641023 PMCID: PMC9040495 DOI: 10.1016/j.jphs.2022.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) remains prevalent worldwide since its onset was confirmed in Wuhan, China in 2019. Vaccines against the causative virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), have shown a preventive effect against the onset and severity of COVID-19, and social and economic activities are gradually recovering. However, the presence of vaccine-resistant variants has been reported, and the development of therapeutic agents for patients with severe COVID-19 and related sequelae remains urgent. Drug repurposing, also called drug repositioning or eco-pharma, is the strategy of using previously approved and safe drugs for a therapeutic indication that is different from their original indication. The risk of severe COVID-19 and mortality increases with advancing age, cardiovascular disease, hypertension, diabetes, and cancer. We have reported three protein-protein interactions that are related to heart failure, and recently identified that one mechanism increases the risk of SARS-CoV-2 infection in mammalian cells. This review outlines the global efforts and outcomes of drug repurposing research for the treatment of severe COVID-19. It also discusses our recent finding of a new protein-protein interaction that is common to COVID-19 aggravation and heart failure.
Collapse
Affiliation(s)
- Yuri Kato
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Kazuhiro Nishiyama
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan
| | - Akiyuki Nishimura
- Division of Cardiocirculatory Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Physiological Sciences, SOKENDAI, Okazaki, Aichi, Japan
| | - Takamasa Noda
- Department of Psychiatry, National Center of Neurology and Psychiatry, Tokyo, Japan; Integrative Brain Imaging Center, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Neuropsychopharmacology, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan; Department of Brain Bioregulatory Science, The Jikei University Graduate School of Medicine, Tokyo, Japan
| | - Kaori Okabe
- Department of Psychiatry, National Center of Neurology and Psychiatry, Tokyo, Japan
| | - Takahiro Kusakabe
- Laboratory of Insect Genome Science, Graduate School of Bioresource and Bioenvironmental Sciences, Kyushu University, Fukuoka, Japan
| | - Yasunari Kanda
- Division of Pharmacology, National Institute of Health Sciences, Kawasaki, Japan
| | - Motohiro Nishida
- Department of Physiology, Graduate School of Pharmaceutical Science, Kyushu University, Fukuoka, Japan; Division of Cardiocirculatory Signaling, National Institute for Physiological Sciences, National Institutes of Natural Sciences, Okazaki, Aichi, Japan; Department of Creative Research, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Okazaki, Aichi, Japan.
| |
Collapse
|
38
|
Fonseca PLC, Moreira FRR, de Souza RM, Guimarães NR, Carvalho NO, Adelino TER, Alves HJ, Alvim LB, Candido DS, Coelho HP, Costa AVB, Costa WC, de Carvalho AF, de Faria BWF, de Lima AB, de Oliveira ES, de Souza CSA, de Souza FG, Dias RC, Geddes VEV, Godinho IP, Gonçalves AL, Lourenço KL, Magalhães RDM, Malta FSV, Medeiros ELA, Mendes FS, Mendes PHBDP, Mendonça CPTB, Menezes AL, Menezes D, Menezes MT, Miguita L, Moreira RG, Peixoto RB, Queiroz DC, Ribeiro AA, Ribeiro APDB, Saliba JW, Sato HI, Silva JDP, Silva NP, Faria NR, Teixeira SMR, da Fonseca FG, Fernandes APSM, Zauli DAG, Januario JN, de Oliveira JS, Iani FCDM, de Aguiar RS, de Souza RP. Tracking the turnover of SARS-CoV-2 VOCs Gamma to Delta in a Brazilian state (Minas Gerais) with a high-vaccination status. Virus Evol 2022; 8:veac064. [PMID: 35996592 PMCID: PMC9384558 DOI: 10.1093/ve/veac064] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 06/24/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
The emergence and global dissemination of Severe Acute Respiratory Syndrome virus 2 (SARS-CoV-2) variants of concern (VOCs) have been described as the main factor driving the Coronavirus Disease 2019 pandemic. In Brazil, the Gamma variant dominated the epidemiological scenario during the first period of 2021. Many Brazilian regions detected the Delta variant after its first description and documented its spread. To monitor the introduction and spread of VOC Delta, we performed Polymerase Chain Reaction (PCR) genotyping and genome sequencing in ten regional sentinel units from June to October 2021 in the State of Minas Gerais (MG). We documented the introduction and spread of Delta, comprising 70 per cent of the cases 8 weeks later. Comparing the viral loads of the Gamma and Delta dominance periods, we provide additional evidence that the latter is more transmissible. The spread and dominance of Delta did not culminate in the increase in cases and deaths, suggesting that the vaccination may have restrained the epidemic growth. Analysis of 224 novel Delta genomes revealed that Rio de Janeiro state was the primary source for disseminating this variant in the state of MG. We present the establishment of Delta, providing evidence of its enhanced transmissibility and showing that this variant shift did not aggravate the epidemiological scenario in a high immunity setting.
Collapse
Affiliation(s)
- Paula L C Fonseca
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Filipe R R Moreira
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Av. Carlos Chagas Filho 373, Cidade Universitaria, Rio de Janeiro 21941-902, Rio de Janeiro, Brazil
| | - Rafael M de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Natália R Guimarães
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Nara O Carvalho
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Talita E R Adelino
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Hugo J Alves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Luige B Alvim
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Darlan S Candido
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford OX13SZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar 470, Jardim América, São Paulo 05403000, São Paulo, Brazil
| | - Helena P Coelho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Alana V B Costa
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Walyson C Costa
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Alex F de Carvalho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Bruna W F de Faria
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Aline B de Lima
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Eneida S de Oliveira
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Carolina S A de Souza
- Pan American Health Organization—PAHO, Av. Das Nações SEN, Asa Norte, Brasilia 70312970, Brazil
| | - Fernanda G de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Rillery C Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Victor E V Geddes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Igor P Godinho
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Alessandro L Gonçalves
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Karine L Lourenço
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Rubens D M Magalhães
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Frederico S V Malta
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Eva L A Medeiros
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Rodovia Papa João Paulo II 4143. Edifício Minas Gerais, Cidade Administrativa, Serra verde, Belo Horizonte 31630900, Minas Gerais, Brazil
| | - Fernanda S Mendes
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Pedro H B de P Mendes
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Cristiane P T B Mendonça
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Andre L Menezes
- Secretaria Municipal de Saúde de Belo Horizonte, Av. Afonso Pena 2336, Funcionários, Belo Horizonte 30130-040, Minas Gerais, Brazil
| | - Diego Menezes
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Mariane T Menezes
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
| | - Lucyene Miguita
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Rennan G Moreira
- Centro de Laboratórios Multiusuários, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Renata B Peixoto
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Daniel C Queiroz
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| | - Adriana A Ribeiro
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Ana Paula de B Ribeiro
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Juliana W Saliba
- Pan American Health Organization—PAHO, Av. Das Nações SEN, Asa Norte, Brasilia 70312970, Brazil
| | - Hugo I Sato
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Joice do P Silva
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - Natiely P Silva
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Nuno R Faria
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, Exhibition Rd, South Kensington, London SW7 2BX, UK
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford OX13SZ, UK
- Instituto de Medicina Tropical, Faculdade de Medicina da Universidade de São Paulo, Av. Dr. Enéas Carvalho de Aguiar 470, Jardim América, São Paulo 05403000, São Paulo, Brazil
| | - Santuza M R Teixeira
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Flávio G da Fonseca
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Ana Paula S M Fernandes
- Centro de Tecnologia de Vacinas, Universidade Federal de Minas Gerais, Rua Professor José Vieira de Mendonça 770, Engenho Nogueira, Belo Horizonte 31310260, Minas Gerais, Brazil
| | - Danielle A G Zauli
- Instituto Hermes Pardini, Av. das Nações 2448, Distrito Industrial, Vespasiano 33201003, Minas Gerais, Brazil
| | - José Nélio Januario
- Núcleo de Ações e Pesquisa em Apoio Diagnóstico-Nupad/Faculdade de Medicina/Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Av. Prof. Alfredo Balena 189, Centro, Belo Horizonte 30130-100, Minas Gerais, Brazil
| | - Jaqueline S de Oliveira
- Subsecretaria de Vigilância em Saúde, Secretaria de Estado de Saúde de Minas Gerais, Rodovia Papa João Paulo II 4143. Edifício Minas Gerais, Cidade Administrativa, Serra verde, Belo Horizonte 31630900, Minas Gerais, Brazil
| | - Felipe C de M Iani
- Fundacao Ezequiel Dias, Rua Conde Pereira Carneiro 80, Gameleira, Belo Horizonte 30510-010, Minas Gerais, Brazil
| | - Renato S de Aguiar
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
- Instituto D’OR de Pesquisa e Ensino, Rio de Janeiro 22281100, Rio de Janeiro, Brazil
| | - Renan P de Souza
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270901, Minas Gerais, Brazil
| |
Collapse
|
39
|
Ghosh A, Kar PK, Gautam A, Gupta R, Singh R, Chakravarti R, Ravichandiran V, Ghosh Dastidar S, Ghosh D, Roy S. An insight into SARS-CoV-2 structure, pathogenesis, target hunting for drug development and vaccine initiatives. RSC Med Chem 2022; 13:647-675. [PMID: 35814927 PMCID: PMC9215161 DOI: 10.1039/d2md00009a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 01/27/2023] Open
Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been confirmed to be a new coronavirus having 79% and 50% similarity with SARS-CoV and MERS-CoV, respectively. For a better understanding of the features of the new virus SARS-CoV-2, we have discussed a possible correlation between some unique features of the genome of SARS-CoV-2 in relation to pathogenesis. We have also reviewed structural druggable viral and host targets for possible clinical application if any, as cases of reinfection and compromised protection have been noticed due to the emergence of new variants with increased infectivity even after vaccination. We have also discussed the types of vaccines that are being developed against SARS-CoV-2. In this review, we have tried to give a brief overview of the fundamental factors of COVID-19 research like basic virology, virus variants and the newly emerging techniques that can be applied to develop advanced treatment strategies for the management of COVID-19 disease.
Collapse
Affiliation(s)
- Arijit Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research Kolkata India
- Department of Chemistry, University of Calcutta Kolkata India
- Netaji Subhas Chandra Bose Cancer Research institute 3081, Nayabad Kolkata-700094 India
| | - Paritosh K Kar
- Foundation on Tropical Diseases & Health Research Development, A Mission on Charitable Health Care Unit Balichak CT, Paschim Medinipur West Bengal 721 124 India
| | - Anupam Gautam
- Institute for Bioinformatics and Medical Informatics, University of Tübingen Sand 14 72076 Tübingen Germany
- International Max Planck Research School "From Molecules to Organisms", Max Planck Institute for Biology Tübingen Max-Planck-Ring 5 72076 Tübingen Germany
| | - Rahul Gupta
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology Kolkata India
| | - Rajveer Singh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research Kolkata India
| | - Rudra Chakravarti
- Department of Natural Products, National Institute of Pharmaceutical Education and Research Kolkata India
| | - Velayutham Ravichandiran
- Department of Natural Products, National Institute of Pharmaceutical Education and Research Kolkata India
| | | | - Dipanjan Ghosh
- Department of Natural Products, National Institute of Pharmaceutical Education and Research Kolkata India
| | - Syamal Roy
- Infectious Diseases and Immunology Division, CSIR-Indian Institute of Chemical Biology Kolkata India
| |
Collapse
|
40
|
Lai FTT, Huang L, Peng K, Li X, Chui CSL, Wan EYF, Wong CKH, Chan EWY, Hung IFN, Wong ICK. Post-Covid-19-vaccination adverse events and healthcare utilization among individuals with or without previous SARS-CoV-2 infection. J Intern Med 2022; 291:864-869. [PMID: 35043503 PMCID: PMC9303328 DOI: 10.1111/joim.13453] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BACKGROUND Post-marketing pharmacovigilance data are scant on the safety of Covid-19 vaccines among people with previous SARS-CoV-2 infection compared with ordinary vaccine recipients. We compared the post-vaccination adverse events of special interests (AESI), accident and emergency room (A&E) visit, and hospitalization between these two groups. METHODS We conducted a retrospective cohort study using a territory-wide public healthcare database with population-based vaccination records in Hong Kong. RESULTS In total, 3922 vaccine recipients with previous SARS-CoV-2 infection and 1,137,583 vaccine recipients without previous SARS-CoV-2 infection were included. No significant association was observed between previous SARS-CoV-2 infection and AESI or hospitalization. Previous SARS-CoV-2 infection was significantly associated with a lower risk of A&E visit (CoronaVac: hazard ratios [HR] = 0.56, 95% confidence intervals [CI]: 0.32-0.99; Comirnaty: HR = 0.62, 95% CI: 0.47-0.82). CONCLUSION No safety signal of Covid-19 vaccination was detected from the comparison between vaccine recipients with previous SARS-CoV-2 infection and those without infection.
Collapse
Affiliation(s)
- Francisco Tsz Tsun Lai
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Lei Huang
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Kuan Peng
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Xue Li
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China.,Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Celine Sze Ling Chui
- Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China.,School of Nursing, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Eric Yuk Fai Wan
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China.,Department of Family Medicine and Primary Care, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Carlos King Ho Wong
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China.,Department of Family Medicine and Primary Care, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Esther Wai Yin Chan
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China
| | - Ivan Fan Ngai Hung
- Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Ian Chi Kei Wong
- Centre for Safe Medication Practice and Research, Department of Pharmacology and Pharmacy, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China.,Laboratory of Data Discovery for Health (D24H), Hong Kong Science Park, Hong Kong Science and Technology Park, Hong Kong SAR, China.,Research Department of Practice and Policy, School of Pharmacy, University College London, London, United Kingdom
| |
Collapse
|
41
|
Souza PFN, Mesquita FP, Amaral JL, Landim PGC, Lima KRP, Costa MB, Farias IR, Belém MO, Pinto YO, Moreira HHT, Magalhaes ICL, Castelo-Branco DSCM, Montenegro RC, de Andrade CR. The spike glycoprotein of SARS-CoV-2: A review of how mutations of spike glycoproteins have driven the emergence of variants with high transmissibility and immune escape. Int J Biol Macromol 2022; 208:105-125. [PMID: 35300999 PMCID: PMC8920968 DOI: 10.1016/j.ijbiomac.2022.03.058] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/08/2022] [Accepted: 03/10/2022] [Indexed: 12/23/2022]
Abstract
Late in 2019, SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2) emerged, causing an unknown type of pneumonia today called coronaviruses disease 2019 (COVID-19). COVID-19 is still an ongoing global outbreak that has claimed and threatened many lives worldwide. Along with the fastest vaccine developed in history to fight SARS-CoV-2 came a critical problem, SARS-CoV-2. These new variants are a result of the accumulation of mutations in the sequence and structure of spike (S) glycoprotein, which is by far the most critical protein for SARS-CoV-2 to recognize cells and escape the immune system, in addition to playing a role in SARS-CoV-2 infection, pathogenicity, transmission, and evolution. In this review, we discuss mutation of S protein and how these mutations have led to new variants that are usually more transmissible and can thus mitigate the immunity produced by vaccination. Here, analysis of S protein sequences and structures from variants point out the mutations among them, how they emerge, and the behavior of S protein from each variant. This review brings details in an understandable way about how the variants of SARS-CoV-2 are a result of mutations in S protein, making them more transmissible and even more aggressive than their relatives.
Collapse
Affiliation(s)
- Pedro F N Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil; Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil.
| | - Felipe P Mesquita
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Jackson L Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Patrícia G C Landim
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Karollyny R P Lima
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Brazil
| | - Marília B Costa
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Izabelle R Farias
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Mônica O Belém
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| | - Yago O Pinto
- Medical Education Institution-Idomed, Canindé, Ceará, Brazil
| | | | | | - Débora S C M Castelo-Branco
- Department of Pathology and Legal Medicine, Postgraduate Program in Medical Microbiology, Group of Applied Medical Microbiology, Federal University of Ceará, Fortaleza, Ceará, Brazil
| | - Raquel C Montenegro
- Drug research and Development Center, Department of Medicine, Federal University of Ceará, Brazil
| | - Claudia R de Andrade
- Laboratory of Translational Research, Christus University Center, Fortaleza, Ceará 60192, Brazil
| |
Collapse
|
42
|
Massard M, Eftimie R, Perasso A, Saussereau B. A multi-strain epidemic model for COVID-19 with infected and asymptomatic cases: application to French data. J Theor Biol 2022; 545:111117. [PMID: 35513167 PMCID: PMC9059428 DOI: 10.1016/j.jtbi.2022.111117] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 10/27/2022]
Abstract
Many SARS-CoV-2 variants have appeared over the last months, and many more will continue to appear. Understanding the competition between these different variants could help make future predictions on the evolution of epidemics. In this study we use a mathematical model to investigate the impact of three different SARS-CoV-2 variants on the spread of COVID-19 across France, between January-May 2021 (before vaccination was extended to the full population). To this end, we use the data from Geodes (produced by Public Health France) and a particle swarm optimisation algorithm, to estimate the model parameters and further calculate a value for the basic reproduction number R0. Sensitivity and uncertainty analysis is then used to better understand the impact of estimated parameter values on the number of infections leading to both symptomatic and asymptomatic individuals. The results confirmed that, as expected, the alpha, beta and gamma variants are more transmissible than the original viral strain. In addition, the sensitivity results showed that the beta/gamma variants could have lead to a larger number of infections in France (of both symptomatic and asymptomatic people).
Collapse
Affiliation(s)
- Mathilde Massard
- Laboratoire de Mathématiques de Besançon, University of Bourgogne Franche-Comté, UFR ST 16 route de GRAY, 25030 Besançon, France.
| | - Raluca Eftimie
- Laboratoire de Mathématiques de Besançon, University of Bourgogne Franche-Comté, UFR ST 16 route de GRAY, 25030 Besançon, France.
| | - Antoine Perasso
- Laboratoire Chrono-environnement, University of Bourgogne Franche-Comté, UFR ST 16 route de GRAY, 25030 Besançon, France.
| | - Bruno Saussereau
- Laboratoire de Mathématiques de Besançon, University of Bourgogne Franche-Comté, UFR ST 16 route de GRAY, 25030 Besançon, France.
| |
Collapse
|
43
|
Ren X, Zhou J, Guo J, Hao C, Zheng M, Zhang R, Huang Q, Yao X, Li R, Jin Y. Reinfection in patients with COVID-19: a systematic review. Glob Health Res Policy 2022; 7:12. [PMID: 35488305 PMCID: PMC9051013 DOI: 10.1186/s41256-022-00245-3] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 04/03/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND With the continuation of the COVID-19 pandemic, some COVID-19 patients have become reinfected with the virus. Viral gene sequencing has found that some of these patients were reinfected by the different and others by same strains. This has raised concerns about the effectiveness of immunity after infection and the reliability of vaccines. To this end, we conducted a systematic review to assess the characteristics of patients with reinfection and possible causes. METHODS A systematic search was conducted across eight databases: PubMed, Embase, Web of Science, The Cochrane Library, CNKI, WanFang, VIP and SinoMed from December 1, 2019 to September 1, 2021. The quality of included studies were assessed using JBI critical appraisal tools and Newcastle-Ottawa Scale. RESULTS This study included 50 studies from 20 countries. There were 118 cases of reinfection. Twenty-five patients were reported to have at least one complication. The shortest duration between the first infection and reinfection was 19 days and the longest was 293 days. During the first infection and reinfection, cough (51.6% and 43.9%) and fever (50% and 30.3%) were the most common symptoms respectively. Nine patients recovered, seven patients died, and five patients were hospitalized, but 97 patients' prognosis were unknown. B.1 is the most common variant strain at the first infection. B.1.1.7, B.1.128 and B.1.351 were the most common variant strains at reinfection. Thirty-three patients were infected by different strains and 9 patients were reported as being infected with the same strain. CONCLUSIONS Our research shows that it is possible for rehabilitated patients to be reinfected by SARS-COV-2. To date, the causes and risk factors of COVID-19 reinfection are not fully understood. For patients with reinfection, the diagnosis and management should be consistent with the treatment of the first infection. The public, including rehabilitated patients, should be fully vaccinated, wear masks in public places, and pay attention to maintaining social distance to avoid reinfection with the virus.
Collapse
Affiliation(s)
- Xiangying Ren
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
- College of Nursing and Health, Henan University, Kaifeng, Henan China
| | - Jie Zhou
- School of Nursing, Wuhan University, Wuhan, China
| | - Jing Guo
- Department of Acupuncture Rehabilitation, The Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunmei Hao
- The First Clinical College of Wuhan University, Wuhan, Hubei China
| | - Mengxue Zheng
- The First Clinical College of Wuhan University, Wuhan, Hubei China
| | - Rong Zhang
- Department of Neurotumor Disease Diagnosis and Treatment Center, Taihe Hospital, Hubei University of Medicine, Shiyan, China
| | - Qiao Huang
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaomei Yao
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON Canada
- Center for Clinical Practice Guideline Conduction and Evaluation, Children’s Hospital of Fudan University, Shanghai, China
| | - Ruiling Li
- College of Nursing and Health, Henan University, Kaifeng, Henan China
| | - Yinghui Jin
- Center for Evidence-Based and Translational Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| |
Collapse
|
44
|
Martínez-González B, Soria ME, Vázquez-Sirvent L, Ferrer-Orta C, Lobo-Vega R, Mínguez P, de la Fuente L, Llorens C, Soriano B, Ramos R, Cortón M, López-Rodríguez R, García-Crespo C, Gallego I, de Ávila AI, Gómez J, Enjuanes L, Salar-Vidal L, Esteban J, Fernandez-Roblas R, Gadea I, Ayuso C, Ruíz-Hornillos J, Verdaguer N, Domingo E, Perales C. SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes. Microbiol Spectr 2022; 10:e0022122. [PMID: 35348367 PMCID: PMC9045161 DOI: 10.1128/spectrum.00221-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/25/2022] [Indexed: 12/15/2022] Open
Abstract
Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.
Collapse
Affiliation(s)
- Brenda Martínez-González
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - María Eugenia Soria
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Lucía Vázquez-Sirvent
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Cristina Ferrer-Orta
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Rebeca Lobo-Vega
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Pablo Mínguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Lorena de la Fuente
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
- Bioinformatics Unit, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carlos Llorens
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Beatriz Soriano
- Biotechvana, “Scientific Park”, Universidad de Valencia, Valencia, Spain
| | - Ricardo Ramos
- Unidad de Genómica, “Scientific Park of Madrid”, Campus de Cantoblanco, Madrid, Spain
| | - Marta Cortón
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Rosario López-Rodríguez
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos García-Crespo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Isabel Gallego
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Jordi Gómez
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Instituto de Parasitología y Biomedicina ‘López-Neyra’ (CSIC), Parque Tecnológico Ciencias de la Salud, Granada, Spain
| | - Luis Enjuanes
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Llanos Salar-Vidal
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Jaime Esteban
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ricardo Fernandez-Roblas
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
| | - Carmen Ayuso
- Department of Genetics & Genomics, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centre for Biomedical Network Research on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Madrid, Spain
| | - Javier Ruíz-Hornillos
- Allergy Unit, Hospital Infanta Elena, Valdemoro, Madrid, Spain
- Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Faculty of Medicine, Universidad Francisco de Vitoria, Madrid, Spain
| | - Nuria Verdaguer
- Structural Biology Department, Institut de Biología Molecular de Barcelona CSIC, Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular “Severo Ochoa” (CSIC-UAM), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
| | - Celia Perales
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid (IIS-FJD, UAM), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| |
Collapse
|
45
|
Ballesteros-Sanabria L, Pelaez-Prestel HF, Ras-Carmona A, Reche PA. Resilience of Spike-Specific Immunity Induced by COVID-19 Vaccines against SARS-CoV-2 Variants. Biomedicines 2022; 10:biomedicines10050996. [PMID: 35625733 PMCID: PMC9138591 DOI: 10.3390/biomedicines10050996] [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: 04/07/2022] [Revised: 04/20/2022] [Accepted: 04/22/2022] [Indexed: 12/10/2022] Open
Abstract
The outbreak of SARS-CoV-2 leading to the declaration of the COVID-19 global pandemic has led to the urgent development and deployment of several COVID-19 vaccines. Many of these new vaccines, including those based on mRNA and adenoviruses, are aimed to generate neutralizing antibodies against the spike glycoprotein, which is known to bind to the receptor angiotensin converting enzyme 2 (ACE2) in host cells via the receptor-binding domain (RBD). Antibodies binding to this domain can block the interaction with the receptor and prevent viral entry into the cells. Additionally, these vaccines can also induce spike-specific T cells which could contribute to providing protection against the virus. However, the emergence of new SARS-CoV-2 variants can impair the immunity generated by COVID-19 vaccines if mutations occur in cognate epitopes, precluding immune recognition. Here, we evaluated the chance of five SARS-CoV-2 variants of concern (VOCs), Alpha, Beta, Gamma, Delta and Omicron, to escape spike-specific immunity induced by vaccines. To that end, we examined the impact of the SARS-CoV-2 variant mutations on residues located on experimentally verified spike-specific epitopes, deposited at the Immune Epitope Database, that are targeted by neutralizing antibodies or recognized by T cells. We found about 300 of such B cell epitopes, which were largely overlapping, and could be grouped into 54 B cell epitope clusters sharing ≥ 7 residues. Most of the B cell epitope clusters map in the RBD domain (39 out of 54) and 20%, 50%, 37%, 44% and 57% of the total are mutated in SARS-CoV-2 Alpha, Beta, Gamma, Delta and Omicron variants, respectively. We also found 234 experimentally verified CD8 and CD4 T cell epitopes that were distributed evenly throughout the spike protein. Interestingly, in each SARS-CoV-2 VOC, over 87% and 79% of CD8 and CD4 T cell epitopes, respectively, are not mutated. These observations suggest that SARS-CoV-2 VOCs—particularly the Omicron variant—may be prone to escape spike-specific antibody immunity, but not cellular immunity, elicited by COVID-19 vaccines.
Collapse
|
46
|
Giovanetti M, Slavov SN, Fonseca V, Wilkinson E, Tegally H, Patané JSL, Viala VL, San JE, Rodrigues ES, Santos EV, Aburjaile F, Xavier J, Fritsch H, Adelino TER, Pereira F, Leal A, de Melo Iani FC, de Carvalho Pereira G, Vazquez C, Mercedes Estigarribia Sanabria G, de Oliveira EC, Demarchi L, Croda J, dos Santos Bezerra R, de Lima LPO, Martins AJ, dos Santos Barros CR, Marqueze EC, de Souza Todao Bernardino J, Moretti DB, Brassaloti RA, de Lello Rocha Campos Cassano R, Mariani PDSC, Kitajima JP, Santos B, Proto-Siqueira R, Cantarelli VV, Tosta S, Nardy VB, de Oliveira da Silva LR, Kelly Astete Gómez M, Lima JG, Ribeiro AA, Guimarães NR, Watanabe LT, Da Silva LB, da Silva Ferreira R, da Penha MPF, Ortega MJ, de la Fuente AG, Villalba S, Torales J, Gamarra ML, Aquino C, Martínez Figueredo GP, Fava WS, Motta-Castro ARC, Venturini J, de Oliveira SMDVL, Gonçalves CCM, do Carmo Debur Rossa M, Becker GN, Presibella MM, Marques NQ, Riediger IN, Raboni S, Coelho GM, Cataneo AHD, Zanluca C, dos Santos CND, Assato PA, da Costa FADS, Poleti MD, Lesbon JCC, Mattos EC, Banho CA, Sacchetto L, Moraes MM, Grotto RMT, Souza-Neto JA, Nogueira ML, Fukumasu H, Coutinho LL, Calado RT, Neto RM, de Filippis AMB, da Cunha RV, Freitas C, Peterka CRL, de Fátima Rangel Fernandes C, de Araújo WN, do Carmo Said RF, Almiron M, de Albuquerque e Melo CFC, Lourenço J, de Oliveira T, Holmes EC, Haddad R, Sampaio SC, Elias MC, Kashima S, de Alcantara LCJ, Covas DT. Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2021.10.07.21264644. [PMID: 35378755 PMCID: PMC8978948 DOI: 10.1101/2021.10.07.21264644] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.
Collapse
Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Butantan Institute, São Paulo, Brazil
| | - Vagner Fonseca
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Eduan Wilkinson
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | | | | | - James Emmanuel San
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
| | - Evandra Strazza Rodrigues
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Elaine Vieira Santos
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Flavia Aburjaile
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Joilson Xavier
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Hegger Fritsch
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Talita Emile Ribeiro Adelino
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Felicidade Pereira
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | - Arabela Leal
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | - Felipe Campos de Melo Iani
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Glauco de Carvalho Pereira
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | | | - Gladys Mercedes Estigarribia Sanabria
- Universidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud
- Laboratorio de Biología Molecular, Hospital Regional de Coronel Oviedo
- Ministerio de Salud Pública y Bienestar Social
| | | | - Luiz Demarchi
- Laboratório Central de Saúde Pública do Estado de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Rafael dos Santos Bezerra
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | | | | | | | | | | | | | | | | | | | | | - Vlademir Vicente Cantarelli
- Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Universidade Feevale, Grupo Exame Laboratórios, Rio Grande do Sul, Brazil
| | - Stephane Tosta
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
- Laboratorio Central de Saude Publica da Bahia–LACEN-BA, Salvador, Bahia, Brazil
| | | | | | | | | | - Adriana Aparecida Ribeiro
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Natália Rocha Guimarães
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundac ão Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Takao Watanabe
- Laboratório Central de Saúde Pública do Estado de Mato Grosso, Cuiabá, Brazil
| | | | | | | | | | | | | | - Juan Torales
- Laboratorio Central de Salud Pública, Asunción, Paraguay
| | | | | | - Gloria Patricia Martínez Figueredo
- Universidad Nacional del Caaguazú, Instituto Regional de Investigación en Salud
- Laboratorio de Biología Molecular, Hospital Regional de Coronel Oviedo
- Ministerio de Salud Pública y Bienestar Social
| | | | | | | | | | | | | | | | | | | | | | - Sonia Raboni
- Hospital de Clínicas da Universidade Federal do Paraná, Curitiba, PR
| | | | | | - Camila Zanluca
- Laboratório de Virologia Molecular - Instituto Carlos Chagas/Fiocruz PR, Curitiba, PR
| | | | - Patricia Akemi Assato
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Felipe Allan da Silva da Costa
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Mirele Daiana Poleti
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Jessika Cristina Chagas Lesbon
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Elisangela Chicaroni Mattos
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Cecilia Artico Banho
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Marília Mazzi Moraes
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Rejane Maria Tommasini Grotto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
- Molecular Biology Laboratory, Applied Biotechnology Laboratory, Clinical Hospital of the Botucatu Medical School, Brazil
| | - Jayme A. Souza-Neto
- São Paulo State University (UNESP), School of Agricultural Sciences, Department of Bioprocesses and Biotechnology, Botucatu, Brazil
| | - Maurício Lacerda Nogueira
- Laboratório de Pesquisas em Virologia, Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, São Paulo, Brazil
| | - Luiz Lehmann Coutinho
- University of São Paulo, Centro de Genômica Funcional da ESALQ, Piracicaba, SP, Brazil
| | - Rodrigo Tocantins Calado
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | | | | | | | - Carla Freitas
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS) Brasília, Distrito Federal, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilaçncia em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Distrito Federal, Brazil
| | - Cássia de Fátima Rangel Fernandes
- Departamento de Imunização e Doenças Transmissíveisa/Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil
| | | | | | - Maria Almiron
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Distrito Federal, Brazil
| | | | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
- Biosystems and Integrative Sciences Institute, Universidade de Lisboa, Lisboa, Portugal
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University; Stellenbosch, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, University of Sydney, Sydney, NSW, Australia
| | | | | | | | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
| | - Luiz Carlos Junior de Alcantara
- Laboratório de Flavivírus, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Dimas Tadeu Covas
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, SP, Brazil
- Butantan Institute, São Paulo, Brazil
| |
Collapse
|
47
|
Dong R, Hu T, Zhang Y, Li Y, Zhou XH. Assessing the Transmissibility of the New SARS-CoV-2 Variants: From Delta to Omicron. Vaccines (Basel) 2022; 10:496. [PMID: 35455246 PMCID: PMC9026126 DOI: 10.3390/vaccines10040496] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 02/06/2023] Open
Abstract
Omicron, the latest SARS-CoV-2 Variant of Concern (VOC), first appeared in Africa in November 2021. At present, the question of whether a new VOC will out-compete the currently predominant variant is important for governments seeking to determine if current surveillance strategies and responses are appropriate and reasonable. Based on both virus genomes and daily-confirmed cases, we compare the additive differences in growth rates and reproductive numbers (R0) between VOCs and their predominant variants through a Bayesian framework and phylo-dynamics analysis. Faced with different variants, we evaluate the effects of current policies and vaccinations against VOCs and predominant variants. The model also predicts the date on which a VOC may become dominant based on simulation and real data in the early stage. The results suggest that the overall additive difference in growth rates of B.1.617.2 and predominant variants was 0.44 (95% confidence interval, 95% CI: -0.38, 1.25) in February 2021, and that the VOC had a relatively high R0. The additive difference in the growth rate of BA.1 in the United Kingdom was 6.82 times the difference between Delta and Alpha, and the model successfully predicted the dominating process of Alpha, Delta and Omicron. Current vaccination strategies remain similarly effective against Delta compared to the previous variants. Our model proposes a reliable Bayesian framework to predict the spread trends of VOCs based on early-stage data, and evaluates the effects of public health policies, which may help us better prepare for the upcoming Omicron variant, which is now spreading at an unprecedented speed.
Collapse
Affiliation(s)
- Rui Dong
- Yau Mathematical Sciences Center, Tsinghua University, Beijing 100084, China;
- Yanqi Lake Beijing Institute of Mathematical Sciences and Applications, Beijing 101408, China
| | - Taojun Hu
- Department of Biostatistics, School of Public Health, Peking University, Beijing 100191, China; (T.H.); (Y.Z.)
| | - Yunjun Zhang
- Department of Biostatistics, School of Public Health, Peking University, Beijing 100191, China; (T.H.); (Y.Z.)
| | - Yang Li
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400020, China;
| | - Xiao-Hua Zhou
- Department of Biostatistics, School of Public Health, Peking University, Beijing 100191, China; (T.H.); (Y.Z.)
- Beijing International Center for Mathematical Research, Peking University, Beijing 100191, China
| |
Collapse
|
48
|
Dos Santos VP, Rodrigues A, Dutra G, Bastos L, Mariano D, Mendonça JG, Lobo YJG, Mendes E, Maia G, Machado KDS, Werhli AV, Rocha G, de Lima LHF, de Melo-Minardi R. E-Volve: understanding the impact of mutations in SARS-CoV-2 variants spike protein on antibodies and ACE2 affinity through patterns of chemical interactions at protein interfaces. PeerJ 2022; 10:e13099. [PMID: 35341044 PMCID: PMC8953562 DOI: 10.7717/peerj.13099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 02/21/2022] [Indexed: 01/12/2023] Open
Abstract
Background The SARS-CoV-2 pandemic reverberated, posing health and social hygiene obstacles throughout the globe. Mutant lineages of the virus have concerned scientists because of convergent amino acid alterations, mainly on the viral spike protein. Studies have shown that mutants have diminished activity of neutralizing antibodies and enhanced affinity with its human cell receptor, the ACE2 protein. Methods Hence, for real-time measuring of the impacts caused by variant strains in such complexes, we implemented E-Volve, a tool designed to model a structure with a list of mutations requested by users and return analyses of the variant protein. As a proof of concept, we scrutinized the spike-antibody and spike-ACE2 complexes formed in the variants of concern, B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma), by using contact maps depicting the interactions made amid them, along with heat maps to quantify these major interactions. Results The results found in this study depict the highly frequent interface changes made by the entire set of mutations, mainly conducted by N501Y and E484K. In the spike-Antibody complex, we have noticed alterations concerning electrostatic surface complementarity, breaching essential sites in the P17 and BD-368-2 antibodies. Alongside, the spike-ACE2 complex has presented new hydrophobic bonds. Discussion Molecular dynamics simulations followed by Poisson-Boltzmann calculations corroborate the higher complementarity to the receptor and lower to the antibodies for the K417T/E484K/N501Y (Gamma) mutant compared to the wild-type strain, as pointed by E-Volve, as well as an intensification of this effect by changes at the protein conformational equilibrium in solution. A local disorder of the loop α1'/β1', as well its possible effects on the affinity to the BD-368-2 antibody were also incorporated to the final conclusions after this analysis. Moreover, E-Volve can depict the main alterations in important biological structures, as shown in the SARS-CoV-2 complexes, marking a major step in the real-time tracking of the virus mutant lineages. E-Volve is available at http://bioinfo.dcc.ufmg.br/evolve.
Collapse
Affiliation(s)
- Vitor Pimentel Dos Santos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - André Rodrigues
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Gabriel Dutra
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Luana Bastos
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Diego Mariano
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - José Gutembergue Mendonça
- Laboratory of Quantum and Computational Chemistry, Center of Exact and Natural Sciences, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Yan Jerônimo Gomes Lobo
- Laboratory of Molecular Modeling and Bioinformatics, Campus Sete Lagoas, Department of Exact and Biological Sciences, Universidade Federal de São João del-Rei, Sete Lagoas, MG, Brazil
| | - Eduardo Mendes
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Giovana Maia
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Karina dos Santos Machado
- Computational Biology Laboratory (ComBi-Lab), Center for Computational Sciences-C3, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Adriano Velasque Werhli
- Computational Biology Laboratory (ComBi-Lab), Center for Computational Sciences-C3, Universidade Federal do Rio Grande, Rio Grande, RS, Brazil
| | - Gerd Rocha
- Laboratory of Quantum and Computational Chemistry, Center of Exact and Natural Sciences, Department of Chemistry, Universidade Federal da Paraíba, João Pessoa, PB, Brazil
| | - Leonardo Henrique França de Lima
- Laboratory of Molecular Modeling and Bioinformatics, Campus Sete Lagoas, Department of Exact and Biological Sciences, Universidade Federal de São João del-Rei, Sete Lagoas, MG, Brazil
| | - Raquel de Melo-Minardi
- Laboratory of Bioinformatics and Systems, Institute of Exact Sciences, Department of Computer Science, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| |
Collapse
|
49
|
Cochin M, Luciani L, Touret F, Driouich JS, Petit PR, Moureau G, Baronti C, Laprie C, Thirion L, Maes P, Boudewijns R, Neyts J, de Lamballerie X, Nougairède A. The SARS-CoV-2 Alpha variant exhibits comparable fitness to the D614G strain in a Syrian hamster model. Commun Biol 2022; 5:225. [PMID: 35273335 PMCID: PMC8913834 DOI: 10.1038/s42003-022-03171-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 02/14/2022] [Indexed: 12/14/2022] Open
Abstract
Late 2020, SARS-CoV-2 Alpha variant emerged in United Kingdom and gradually replaced G614 strains initially involved in the global spread of the pandemic. In this study, we use a Syrian hamster model to compare a clinical strain of Alpha variant with an ancestral G614 strain. The Alpha variant succeed to infect animals and to induce a pathology that mimics COVID-19. However, both strains replicate to almost the same level and induced a comparable disease and immune response. A slight fitness advantage is noted for the G614 strain during competition and transmission experiments. These data do not corroborate the epidemiological situation observed during the first half of 2021 in humans nor reports that showed a more rapid replication of Alpha variant in human reconstituted bronchial epithelium. This study highlights the need to combine data from different laboratories using various animal models to decipher the biological properties of newly emerging SARS-CoV-2 variants.
Collapse
Affiliation(s)
- Maxime Cochin
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Léa Luciani
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Jean-Sélim Driouich
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Paul-Rémi Petit
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Grégory Moureau
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Cécile Baronti
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | | | - Laurence Thirion
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Piet Maes
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Epidemiological Virology, Rega Institute, Leuven, Belgium
| | - Robbert Boudewijns
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Johan Neyts
- KU Leuven Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Rega Institute, Leuven, Belgium
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France
| | - Antoine Nougairède
- Unité des Virus Émergents (UVE: Aix-Marseille Univ-IRD 190-Inserm 1207), Marseille, France.
| |
Collapse
|
50
|
Lin L, Chen B, Zhao Y, Wang W, He D. Two waves of COIVD-19 in Brazilian cities and vaccination impact. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:4657-4671. [PMID: 35430833 DOI: 10.3934/mbe.2022216] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BACKGROUNDS Brazil has suffered two waves of Coronavirus Disease 2019 (COVID-19). The second wave, coinciding with the spread of the Gamma variant, was more severe than the first wave. Studies have not yet reached a conclusion on some issues including the extent of reinfection, the infection fatality rate (IFR), the infection attack rate (IAR) and the effects of the vaccination campaign in Brazil, though it was reported that confirmed reinfection was at a low level. METHODS We modify the classical Susceptible-Exposed-Infectious-Recovered (SEIR) model with additional class for severe cases, vaccination and time-varying transmission rates. We fit the model to the severe acute respiratory infection (SARI) deaths, which is a proxy of the COVID-19 deaths, in 20 Brazilian cities with the large number of death tolls. We evaluate the vaccination effect by a contrast of "with" vaccination actual scenario and "without" vaccination in a counterfactual scenario. We evaluate the model performance when the reinfection is absent in the model. RESULTS In the 20 Brazilian cities, the model simulated death matched the reported deaths reasonably well. The effect of the vaccination varies across cities. The estimated median IFR is around 1.2%. CONCLUSION Overall, through this modeling exercise, we conclude that the effects of vaccination campaigns vary across cites and the reinfection is not crucial for the second wave. The relatively high IFR could be due to the breakdown of medical system in many cities.
Collapse
Affiliation(s)
- Lixin Lin
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Boqiang Chen
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Yanji Zhao
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Weiming Wang
- School of Mathematics and Statistics, Huaiyin Normal University, Huaian 223300, China
| | - Daihai He
- Department of Applied Mathematics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| |
Collapse
|