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Liana DF, Novianry V, Andriani A, Mahyarudin M, Astuti P. Disappearance of Imported Cases of Omicron Lineage BA.2.40 in West Kalimantan, Indonesia. IRANIAN JOURNAL OF MEDICAL SCIENCES 2024; 49:176-185. [PMID: 38584647 PMCID: PMC10997853 DOI: 10.30476/ijms.2023.97513.2935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/23/2023] [Accepted: 03/29/2023] [Indexed: 04/09/2024]
Abstract
Background The World Health Organization has declared Omicron as the fifth variant of concern with more than 50 mutations, particularly in the spike protein. Given increased viral infectivity due to mutations, worldwide genomic surveillance and detection of severe acute respiratory syndrome 2 (SARS-CoV-2) is essential. The present study aimed to track Omicron lineage BA.2.40 in West Kalimantan, Indonesia. Methods In May-August 2022, nasopharyngeal swab samples (n=3,642) were collected from international travelers to West Kalimantan (active surveillance), and patients hospitalized due to SARS-CoV-2 infection (baseline surveillance). The samples were tested for Omicron lineages based on ORF1ab, N, and HV69-70del genes, followed by whole-genome sequencing. The sequences were then identified using two genomic databases, aligned against the reference genome (Wuhan/Hu-1/2019), and then compared with BA.2.40 lineage detected across the world. Phylogenetic analysis between the samples and other SARS-CoV-2 isolates was performed using molecular evolutionary genetics analysis software. Results Based on the genomic databases, 10 isolates were identified as BA.2.40. All samples tested positive for the ORF1ab and N genes, but negative for the HV69-70del gene, which is a marker to detect the Omicron variant. Phylogenetic analysis showed the isolates were closely related to an isolate from Malaysia, an area dominated by BA.2.40. Conclusion Omicron lineage BA.2.40 has no HV69-70 deletion in the spike protein, a marker used to screen for the Omicron variant. BA.2.40 showed a high similarity to an isolate from Malaysia and was detected only during certain periods, indicating the effect of internationally imported cases.
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Affiliation(s)
- Delima Fajar Liana
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Virhan Novianry
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Andriani Andriani
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Mahyarudin Mahyarudin
- Department of Microbiology, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
| | - Puji Astuti
- Department of Biochemistry and Biomolecular, School of Medicine, Universitas Tanjungpura, Pontianak, Indonesia
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Lan PD, Nissley DA, O’Brien EP, Nguyen TT, Li MS. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J Chem Phys 2024; 160:055101. [PMID: 38310477 PMCID: PMC11223169 DOI: 10.1063/5.0188053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Accepted: 01/08/2024] [Indexed: 02/05/2024] Open
Abstract
The binding of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein to the host cell receptor angiotensin-converting enzyme 2 (ACE2) is the first step in human viral infection. Therefore, understanding the mechanism of interaction between RBD and ACE2 at the molecular level is critical for the prevention of COVID-19, as more variants of concern, such as Omicron, appear. Recently, atomic force microscopy has been applied to characterize the free energy landscape of the RBD-ACE2 complex, including estimation of the distance between the transition state and the bound state, xu. Here, using a coarse-grained model and replica-exchange umbrella sampling, we studied the free energy landscape of both the wild type and Omicron subvariants BA.1 and XBB.1.5 interacting with ACE2. In agreement with experiment, we find that the wild type and Omicron subvariants have similar xu values, but Omicron binds ACE2 more strongly than the wild type, having a lower dissociation constant KD.
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Affiliation(s)
| | - Daniel A. Nissley
- Department of Statistics, University of Oxford, Oxford Protein Bioinformatics Group, Oxford OX1 2JD, United Kingdom
| | | | - Toan T. Nguyen
- Key Laboratory for Multiscale Simulation of Complex Systems and Department of Theoretical Physics, Faculty of Physics, University of Science, Vietnam National University - Hanoi, 334 Nguyen Trai Street, Thanh Xuan District, Hanoi 11400, Vietnam
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland
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Sarkar A, Omar S, Alshareef A, Fanous K, Sarker S, Alroobi H, Zamir F, Yousef M, Zakaria D. The relative prevalence of the Omicron variant within SARS-CoV-2 infected cohorts in different countries: A systematic review. Hum Vaccin Immunother 2023; 19:2212568. [PMID: 37254497 PMCID: PMC10234134 DOI: 10.1080/21645515.2023.2212568] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 05/08/2023] [Indexed: 06/01/2023] Open
Abstract
The Omicron variant of SARS-CoV-2 was detected in October 2021 and exhibited high transmissibility, immune evasion, and reduced severity when compared to the earlier variants. The lesser vaccine effectiveness against Omicron and its reduced severity created vaccination hesitancy among the public. This review compiled data reporting the relative prevalence of Omicron as compared to the early variants to give an insight into the existing variants, which may shape the decisions regarding the targets of the newly developed vaccines. Complied data revealed more than 90% prevalence within the infected cohorts in some countries. The BA.1 subvariant predominated over the BA.2 during the early stages of the Omicron wave. Moreover, BA.4/BA.5 subvariants were detected in South Africa, USA and Italy between October 2021 and April 2022. It is therefore important to develop vaccines that protect against Omicron as well as the early variants, which are known to cause more severe complications.
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Affiliation(s)
| | - Sara Omar
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Aya Alshareef
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Kareem Fanous
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Shaunak Sarker
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Hasan Alroobi
- Medical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Fahad Zamir
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Mahmoud Yousef
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
| | - Dalia Zakaria
- Premedical Division, Weill Cornell Medicine-Qatar, Doha, Qatar
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Zaman N, Parvaiz N, Gul F, Yousaf R, Gul K, Azam SS. Dynamics of water-mediated interaction effects on the stability and transmission of Omicron. Sci Rep 2023; 13:20894. [PMID: 38017052 PMCID: PMC10684572 DOI: 10.1038/s41598-023-48186-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Accepted: 11/23/2023] [Indexed: 11/30/2023] Open
Abstract
SARS-Cov-2 Omicron variant and its highly transmissible sublineages amidst news of emerging hybrid variants strengthen the evidence of its ability to rapidly spread and evolve giving rise to unprecedented future waves. Owing to the presence of isolated RBD, monomeric and trimeric Cryo-EM structures of spike protein in complex with ACE2 receptor, comparative analysis of Alpha, Beta, Gamma, Delta, and Omicron assist in a rational assessment of their probability to evolve as new or hybrid variants in future. This study proposes the role of hydration forces in mediating Omicron function and dynamics based on a stronger interplay between protein and solvent with each Covid wave. Mutations of multiple hydrophobic residues into hydrophilic residues underwent concerted interactions with water leading to variations in charge distribution in Delta and Omicron during molecular dynamics simulations. Moreover, comparative analysis of interacting moieties characterized a large number of mutations lying at RBD into constrained, homologous and low-affinity groups referred to as mutational drivers inferring that the probability of future mutations relies on their function. Furthermore, the computational findings reveal a significant difference in angular distances among variants of concern due 3 amino acid insertion (EPE) in Omicron variant that not only facilitates tight domain organization but also seems requisite for characterization of mutational processes. The outcome of this work signifies the possible relation between hydration forces, their impact on conformation and binding affinities, and viral fitness that will significantly aid in understanding dynamics of drug targets for Covid-19 countermeasures. The emerging scenario is that hydration forces and hydrophobic interactions are crucial variables to probe in mutational analysis to explore conformational landscape of macromolecules and reveal the molecular origins of protein behaviors.
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Affiliation(s)
- Naila Zaman
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Nousheen Parvaiz
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Fouzia Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Rimsha Yousaf
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Kainat Gul
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Syed Sikander Azam
- Computational Biology Lab, National Center for Bioinformatics (NCB), Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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Dsouza N, C SK. Predicting the changes in neutralizing antibody interaction with G protein derived from Bangladesh isolates of Nipah virus: molecular dynamics based approach. J Biomol Struct Dyn 2023:1-11. [PMID: 37643003 DOI: 10.1080/07391102.2023.2252084] [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: 06/10/2023] [Accepted: 08/18/2023] [Indexed: 08/31/2023]
Abstract
The infectious Nipah virus (NiV) is categorized into NiV-M (Malaysia) and NiV-B (Bangladesh) groups based on its genome comparison, pathogenicity, and mortality rate. The development of therapeutic molecules has used NiV-M-derived data in multiple studies than NiV-B. In continuation with this, the protein level investigation is also less explored to understand the interaction with therapeutic neutralizing antibodies for NiV-B. So, this study focuses on understanding the impact of NiV-B-specific mutations on the interaction of therapeutic neutralizing antibodies with the G protein. The population-based comparative analysis of NiV-B G protein sequences with NiV-M sequence identified twenty-six mutations. These predominantly polar mutations were then used to model the mutant protein (G_MT). In a comparative study, the G protein G_MT and reference protein G_WT (Malaysian origin) were subjected to a protein docking with neutralizing human monoclonal antibody HENV26. The binding affinity and the free binding energy of the glycoprotein in complex with G-WT and G_MT were calculated using PRODIGY and MM/PBSA tools respectively. Based on the PRODIGY report, G-WT showed stronger binding (-13.8 kcal/mol) compared to that of the G_MT (-9.0 kcal/mol) with the HENV26 antibody. The stability of the complexes was evaluated using MM/PBSA which showed higher binding energy with HENV26 for G_WT (-75.11 kcal/mol) in contrast to G_MT (-41.66 kcal/mol). The results indicate that the mutant G protein has a reduced ability to bind to neutralizing antibodies, resulting in a decreased effectiveness against strains carrying these mutations.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Norine Dsouza
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India
- Department of Biotechnology, St. Xavier's College, Mumbai, India
| | - Selvaa Kumar C
- School of Biotechnology and Bioinformatics, D.Y. Patil Deemed to be University, CBD Belapur, Navi Mumbai, India
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Mutational analysis of catalytic site domain of CCHFV L RNA segment. J Mol Model 2023; 29:88. [PMID: 36877258 PMCID: PMC9987378 DOI: 10.1007/s00894-023-05487-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/24/2023] [Indexed: 03/07/2023]
Abstract
INTRODUCTION Crimean-Congo haemorrhagic fever virus (CCHFV) has tripartite RNA genome and is endemic in various countries of Asia, Africa and Europe. METHOD The present study is focused on mutation profiling of CCHFV L segment and phylogenetic clustering of protein dataset into six CCHFV genotypes. RESULTS Phylogenetic tree rooted with NCBI reference sequence (YP_325663.1) indicated less divergence from genotype III and the sequences belonging to same genotypes have shown less divergence among each other. Mutation frequency at 729 mutated positions was calculated and 563, 49, 33, 46 and 38 amino acid positions were found to be mutated at mutation frequency intervals of 0-0.2, 0.21-0.4, 0.41-0.6, 0.61-0.8 and 0.81-1.0 respectively. Thirty-eight highly frequent mutations (0.81-1.0 interval) were found in all genotypes and mapping in L segment (encoded for RdRp) revealed four mutations (V2074I, I2134T/A, V2148A and Q2695H/R) in catalytic site domain and no mutation in OTU domain. Molecular dynamic simulation and in silico analysis showed that catalytic site domain displayed large deviation and fluctuation upon introduction of these point mutations. CONCLUSION Overall study provides strong evidence that OTU domain is highly conserved and less prone to mutation whereas point mutations recorded in catalytic domain have affected the stability of protein and were found to be persistent in the large population.
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Szpulak A, Garlak U, Ćwirko H, Witkowska B, Rombel-Bryzek A, Witkowska D. SARS-CoV-2 and its impact on the cardiovascular and digestive systems - The interplay between new virus variants and human cells. Comput Struct Biotechnol J 2023; 21:1022-1029. [PMID: 36694807 PMCID: PMC9850860 DOI: 10.1016/j.csbj.2023.01.024] [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: 11/05/2022] [Revised: 01/18/2023] [Accepted: 01/18/2023] [Indexed: 01/20/2023] Open
Abstract
Since infection with the novel coronavirus SARS-CoV-2 first emerged in Wuhan, China, in December 2019, the world has been battling the pandemic COVID-19. Patients of all ages and genders are now becoming infected with the new coronavirus variant (Omicron) worldwide, and its subvariants continue to pose a threat to health and life. This article provides a literature review of cardiovascular and gastrointestinal complications resulting from SARS-CoV-2 infection. COVID-19 primarily caused respiratory symptoms, but complications can affect many vital organs. SARS-CoV-2 binds to a human cell receptor (angiotensin-converting enzyme 2 - ACE2) that is predominantly expressed primarily in the heart and gastrointestinal tract, which is why we focused on complications in these organs. Since the high transmissibility of Omicron and its ability to evade the immune system have raised worldwide concern, we have tried to summarise the current knowledge about its development from a structural point of view and to highlight the differences in its binding to human receptors and proteases compared to previous VOC.
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Affiliation(s)
- Angelika Szpulak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Urszula Garlak
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Hanna Ćwirko
- Faculty of Medicine, Wroclaw Medical University, Wybrzeże L. Pasteura 1, 50-367 Wrocław, Poland
| | - Bogusława Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
| | | | - Danuta Witkowska
- Institute of Health Sciences, University of Opole, Katowicka 68, 45-060 Opole, Poland
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Tallei TE, Alhumaid S, AlMusa Z, Fatimawali, Kusumawaty D, Alynbiawi A, Alshukairi AN, Rabaan AA. Update on the omicron sub-variants BA.4 and BA.5. Rev Med Virol 2023; 33:e2391. [PMID: 36017597 PMCID: PMC9539252 DOI: 10.1002/rmv.2391] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/28/2023]
Abstract
Several nations have recently begun to relax their public health protocols, particularly regarding the use of face masks when engaging in outdoor activities. This is because there has been a general trend towards fewer cases of coronavirus disease 2019 (COVID-19). However, new Omicron sub-variants (designated BA.4 and BA.5) have recently emerged. These two subvariants are thought to be the cause of an increase in COVID-19 cases in South Africa, the United States, and Europe. They have also begun to spread throughout Asia. They evolved from the Omicron lineage with characteristics that make them even more contagious and which allow them to circumvent immunity from a previous infection or vaccination. This article reviews a number of scientific considerations about these new variants, including their apparently reduced clinical severity.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of BiologyFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Saad Alhumaid
- Administration of Pharmaceutical CareAl‐Ahsa Health ClusterMinistry of HealthAl‐AhsaSaudi Arabia
| | - Zainab AlMusa
- Infectious Disease SectionInternal Medicine DepartmentKing Fahad Specialist HospitalDammamSaudi Arabia
| | - Fatimawali
- Pharmacy Study ProgramFaculty of Mathematics and Natural SciencesSam Ratulangi UniversityManadoNorth SulawesiIndonesia
| | - Diah Kusumawaty
- Department of BiologyFaculty of Mathematics and Natural Sciences EducationUniversitas Pendidikan IndonesiaBandungIndonesia
| | - Ahlam Alynbiawi
- Infectious Diseases SectionMedical Specialties DepartmentKing Fahad Medical CityRiyadhSaudi Arabia
| | - Abeer N. Alshukairi
- Department of MedicineKing Faisal Specialist Hospital and Research CenterJeddahSaudi Arabia
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
| | - Ali A. Rabaan
- College of MedicineAlfaisal UniversityRiyadhSaudi Arabia
- Molecular Diagnostic LaboratoryJohns Hopkins Aramco HealthcareDhahranSaudi Arabia
- Department of Public Health and NutritionThe University of HaripurHaripurPakistan
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Planchais C, Reyes‐Ruiz A, Lacombe R, Zarantonello A, Lecerf M, Revel M, Roumenina LT, Atanasov BP, Mouquet H, Dimitrov JD. Evolutionary trajectory of receptor binding specificity and promiscuity of the spike protein of SARS-CoV-2. Protein Sci 2022; 31:e4447. [PMID: 36305765 PMCID: PMC9597384 DOI: 10.1002/pro.4447] [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: 07/13/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 01/27/2023]
Abstract
SARS-CoV-2 infects cells by attachment to its receptor-the angiotensin converting enzyme 2 (ACE2). Regardless of the wealth of structural data, little is known about the physicochemical mechanism of interactions of the viral spike (S) protein with ACE2 and how this mechanism has evolved during the pandemic. Here, we applied experimental and computational approaches to characterize the molecular interaction of S proteins from SARS-CoV-2 variants of concern (VOC). Data on kinetics, activation-, and equilibrium thermodynamics of binding of the receptor binding domain (RBD) from VOC with ACE2 as well as data from computational protein electrostatics revealed a profound remodeling of the physicochemical characteristics of the interaction during the evolution. Thus, as compared to RBDs from Wuhan strain and other VOC, Omicron RBD presented as a unique protein in terms of conformational dynamics and types of non-covalent forces driving the complex formation with ACE2. Viral evolution resulted in a restriction of the RBD structural dynamics, and a shift to a major role of polar forces for ACE2 binding. Further, we investigated how the reshaping of the physicochemical characteristics of interaction affects the binding specificity of S proteins. Data from various binding assays revealed that SARS-CoV-2 Wuhan and Omicron RBDs manifest capacity for promiscuous recognition of unrelated human proteins, but they harbor distinct reactivity patterns. These findings might contribute for mechanistic understanding of the viral tropism and capacity to evade immune responses during evolution.
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Affiliation(s)
- Cyril Planchais
- Laboratory of Humoral ImmunologyInstitut Pasteur, Université Paris Cité, INSERM U1222ParisFrance
| | - Alejandra Reyes‐Ruiz
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Robin Lacombe
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Alessandra Zarantonello
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Maxime Lecerf
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Margot Revel
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Lubka T. Roumenina
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
| | - Boris P. Atanasov
- Institute of Organic Chemistry, Bulgarian Academy of SciencesSofiaBulgaria
| | - Hugo Mouquet
- Laboratory of Humoral ImmunologyInstitut Pasteur, Université Paris Cité, INSERM U1222ParisFrance
| | - Jordan D. Dimitrov
- Centre de Recherche des CordeliersINSERM, CNRS, Sorbonne Université, Université de ParisParisFrance
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Konstantinus I, Chiwara D, Ndevaetela EE, Ndarukwa-Phiri V, Garus-oas N, Frans N, Ndumbu P, Shiningavamwe A, van Rooyen G, Schiceya F, Hlahla L, Namundjebo P, Ndozi-Okia I, Chikuse F, Bantiewalu SH, Tjombonde K. Laboratory and field evaluation of the STANDARD Q and Panbio™ SARS-CoV-2 antigen rapid test in Namibia using nasopharyngeal samples. PLoS One 2022; 17:e0269329. [PMID: 36166414 PMCID: PMC9514621 DOI: 10.1371/journal.pone.0269329] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 05/18/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND As new SARS-CoV-2 variants of concern emerge, there is a need to scale up testing to minimize transmission of the Coronavirus disease 2019 (COVID-19). Many countries especially those in the developing world continue to struggle with scaling up reverse transcriptase polymerase reaction (RT-PCR) to detect SARS-CoV-2 due to scarcity of resources. Alternatives such as antigen rapid diagnostics tests (Ag-RDTs) may provide a solution to enable countries scale up testing. METHODS In this study, we evaluated the Panbio™ and STANDARD Q Ag-RDTs in the laboratory using 80 COVID-19 RT-PCR confirmed and 80 negative nasopharyngeal swabs. The STANDARD Q was further evaluated in the field on 112 symptomatic and 61 asymptomatic participants. RESULTS For the laboratory evaluation, both tests had a sensitivity above 80% (Panbio™ = 86% vs STANDARD Q = 88%). The specificity of the Panbio™ was 100%, while that of the STANDARD Q was 99%. When evaluated in the field, the STANDARD Q maintained a high specificity of 99%, however the sensitivity was reduced to 56%. CONCLUSION Using Ag-RDTs in low resource settings will be helpful in scaling-up SARS-CoV-2 testing, however, negative results should be confirmed by RT-PCR where possible to rule out COVID-19 infection.
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Affiliation(s)
| | - Douglas Chiwara
- Department of Quality Assurance, Namibia Institute of Pathology, Windhoek, Namibia
| | - Emmy-Else Ndevaetela
- Division of Epidemiology, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Nathalia! Garus-oas
- Department of Molecular Diagnostics, Namibia Institute of Pathology, Windhoek, Namibia
| | - Ndahafa Frans
- Department of Molecular Diagnostics, Namibia Institute of Pathology, Windhoek, Namibia
| | - Pentikainen Ndumbu
- Department of Molecular Diagnostics, Namibia Institute of Pathology, Windhoek, Namibia
| | - Andreas Shiningavamwe
- Department of Molecular Diagnostics, Namibia Institute of Pathology, Windhoek, Namibia
| | - Gerhard van Rooyen
- Department of Molecular Diagnostics, Namibia Institute of Pathology, Windhoek, Namibia
| | - Ferlin Schiceya
- Division of Case Management, Ministry of Health and Social Services, Windhoek, Namibia
| | - Lindile Hlahla
- Division of Case Management, Ministry of Health and Social Services, Windhoek, Namibia
| | - Pendapala Namundjebo
- Division of Epidemiology, Ministry of Health and Social Services, Windhoek, Namibia
| | - Ifeoma Ndozi-Okia
- Division of Epidemiology, Ministry of Health and Social Services, Windhoek, Namibia
| | - Francis Chikuse
- Division of Epidemiology, Ministry of Health and Social Services, Windhoek, Namibia
| | | | - Kapena Tjombonde
- Department of Research, Namibia Institute of Pathology, Windhoek, Namibia
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Mahmood TB, Hossan MI, Mahmud S, Shimu MSS, Alam MJ, Bhuyan MMR, Emran TB. Missense mutations in spike protein of SARS-CoV-2 delta variant contribute to the alteration in viral structure and interaction with hACE2 receptor. Immun Inflamm Dis 2022; 10:e683. [PMID: 36039645 PMCID: PMC9382871 DOI: 10.1002/iid3.683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 07/17/2022] [Accepted: 07/22/2022] [Indexed: 11/11/2022] Open
Abstract
INTRODUCTION Many of the global pandemics threaten human existence over the decades among which coronavirus disease (COVID-19) is the newest exposure circulating worldwide. The RNA encoded severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is referred as the pivotal agent of this deadly disease that induces respiratory tract infection by interacting host ACE2 receptor with its spike glycoprotein. Rapidly evolving nature of this virus modified into new variants helps in perpetrating immune escape and protection against host defense mechanism. Consequently, a new isolate, delta variant originated from India is spreading perilously at a higher infection rate. METHODS In this study, we focused to understand the conformational and functional significance of the missense mutations found in the spike glycoprotein of SARS-CoV-2 delta variant performing different computational analysis. RESULTS From physiochemical analysis, we found that the acidic isoelectric point of the virus elevated to basic pH level due to the mutations. The targeted mutations were also found to change the interactive bonding pattern and conformational stability analyzed by the molecular dynamic's simulation. The molecular docking study also revealed that L452R and T478K mutations found in the RBD domain of delta variant spike protein contributed to alter interaction with the host ACE2 receptor. CONCLUSIONS Overall, this study provided insightful evidence to understand the morphological and attributive impact of the mutations on SARS-CoV-2 delta variant.
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Affiliation(s)
- Tousif Bin Mahmood
- Department of Biotechnology and Genetic EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Mohammad Imran Hossan
- Department of Biotechnology and Genetic EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Shafi Mahmud
- Department of Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | | | - Md. Jahidul Alam
- Department of Applied Chemistry and Chemical EngineeringNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Md. Mahfuzur Rahman Bhuyan
- Department of Biochemistry and Molecular BiologyNoakhali Science and Technology UniversityNoakhaliBangladesh
| | - Talha Bin Emran
- Department of PharmacyBGC Trust University BangladeshChittagongBangladesh
- Department of PharmacyFaculty of Allied Health Sciences, Daffodil International UniversityDhakaBangladesh
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Mehta SR, Smith DM, Boukadida C, Chaillon A. Comparative Dynamics of Delta and Omicron SARS-CoV-2 Variants across and between California and Mexico. Viruses 2022; 14:1494. [PMID: 35891473 PMCID: PMC9317407 DOI: 10.3390/v14071494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 11/25/2022] Open
Abstract
Evolutionary analysis using viral sequence data can elucidate the epidemiology of transmission. Using publicly available SARS-CoV-2 sequence and epidemiological data, we developed discrete phylogeographic models to interrogate the emergence and dispersal of the Delta and Omicron variants in 2021 between and across California and Mexico. External introductions of Delta and Omicron in the region peaked in early July (2021-07-10 [95% CI: 2021-04-20, 2021-11-01]) and mid-December (2021-12-15 [95% CI: 2021-11-14, 2022-01-09]), respectively, 3 months and 2 weeks after first detection. These repeated introductions coincided with domestic migration events with no evidence of a unique transmission hub. The spread of Omicron was most consistent with gravity centric patterns within Mexico. While cross-border events accounted for only 5.1% [95% CI: 4.3-6] of all Delta migration events, they accounted for 20.6% [95% CI: 12.4-29] of Omicron movements, paralleling the increase in international travel observed in late 2021. Our investigations of the Delta and Omicron epidemics in the California/Mexico region illustrate the complex interplay and the multiplicity of viral and structural factors that need to be considered to limit viral spread, even as vaccination is reducing disease burden. Understanding viral transmission patterns may help intra-governmental responses to viral epidemics.
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Affiliation(s)
- Sanjay R. Mehta
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.R.M.); (D.M.S.)
- Veterans Affairs Health System, San Diego, CA 92093, USA
| | - Davey M. Smith
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.R.M.); (D.M.S.)
- Veterans Affairs Health System, San Diego, CA 92093, USA
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México 14080, Mexico;
| | - Antoine Chaillon
- Department of Medicine, University of California, San Diego, CA 92093, USA; (S.R.M.); (D.M.S.)
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