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Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Alhabibi AM, Hassan AS, Abd Elbaky NM, Eid HA, Khalifa MAAA, Wahab MA, Althoqapy AA, Abdou AE, Zakaria DM, Nassef EM, Kasim SA, Saleh OI, Elsheikh AA, Lotfy M, Sayed A. Impact of Toll-Like Receptor 2 and 9 Gene Polymorphisms on COVID-19: Susceptibility, Severity, and Thrombosis. J Inflamm Res 2023; 16:665-675. [PMID: 36825132 PMCID: PMC9942505 DOI: 10.2147/jir.s394927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/26/2023] [Indexed: 02/18/2023] Open
Abstract
Background Toll-like receptors (TLRs) play an important role in activation of innate and adaptive immune responses. Aim We aimed to detect the association between TLR2 rs5743708 G>A and TLR9 rs5743836 C>T variants and COVID-19 disease susceptibility, severity, and thrombosis by using neutrophil extracellular traps (NETs). Subjects and Methods We included 100 adult COVID-19 patients as well as 100 age- and gender-matched normal controls. Participants were genotyped for TLR2 rs5743708 and TLR9 rs5743836. Citrullinated Histone (H3) was detected as an indicator of NETs. Results The mutant (G/A and C/C) genotypes and (A and C) alleles of TLR2 rs5743708 and TLR9 rs5743836, respectively, have been significantly related to a higher risk of COVID-19 infection, representing a significant risk factor for the severity of COVID-19. There was no significant association between the two variants and citrullinated histone (H3). Conclusion TLR2 rs5743708 and TLR9 rs5743836 variants have been significantly related to a higher risk and severity of COVID-19 infection but had no effect on thrombus formation.
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Affiliation(s)
- Alshaymaa M Alhabibi
- Departments of Clinical Pathology, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt,Correspondence: Alshaymaa M Alhabibi, Tel +201002894075, Email
| | - Asmaa S Hassan
- Departments of Clinical Pathology, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | | | - Hoda Asaad Eid
- Chest Disease, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | | | - Maisa A Wahab
- Vascular Surgery, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Azza Ali Althoqapy
- Medical Microbiology and Immunology Department, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Aml E Abdou
- Medical Microbiology and Immunology Department, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | | | - Eman Mostafa Nassef
- Internal Medicine, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Sammar Ahmed Kasim
- Internal Medicine, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Ola I Saleh
- Radio-Diagnosis, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Asmaa Abdelghany Elsheikh
- Community and Occupational Medicine, Faculty of Medicine for Girls, Al-Azhar University, Cairo, Egypt
| | - Mahmoud Lotfy
- Molecular Biology Department, Genetic Engineering & Biotechnology Research Institute, University of Sadat City, Sadat City, Minufiya, Egypt
| | - Alaa Sayed
- Hormones Department, Medical Research and Clinical Studies Institute, National Research Centre, Cairo, Egypt
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Delshad M, Sanaei MJ, Pourbagheri-Sigaroodi A, Bashash D. Host genetic diversity and genetic variations of SARS-CoV-2 in COVID-19 pathogenesis and the effectiveness of vaccination. Int Immunopharmacol 2022; 111:109128. [PMID: 35963158 PMCID: PMC9359488 DOI: 10.1016/j.intimp.2022.109128] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/15/2022] [Accepted: 08/03/2022] [Indexed: 12/14/2022]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), responsible for the outbreak of coronavirus disease 2019 (COVID-19), has shown a vast range of clinical manifestations from asymptomatic to life-threatening symptoms. To figure out the cause of this heterogeneity, studies demonstrated the trace of genetic diversities whether in the hosts or the virus itself. With this regard, this review provides a comprehensive overview of how host genetic such as those related to the entry of the virus, the immune-related genes, gender-related genes, disease-related genes, and also host epigenetic could influence the severity of COVID-19. Besides, the mutations in the genome of SARS-CoV-2 __leading to emerging of new variants__ per se affect the affinity of the virus to the host cells and enhance the immune escape capacity. The current review discusses these variants and also the latest data about vaccination effectiveness facing the most important variants.
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Affiliation(s)
- Mahda Delshad
- Department of Laboratory Sciences, School of Allied Medical Sciences, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mohammad-Javad Sanaei
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Atieh Pourbagheri-Sigaroodi
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Davood Bashash
- Department of Hematology and Blood Banking, School of Allied Medical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Sun C, Xie C, Bu GL, Zhong LY, Zeng MS. Molecular characteristics, immune evasion, and impact of SARS-CoV-2 variants. Signal Transduct Target Ther 2022; 7:202. [PMID: 35764603 PMCID: PMC9240077 DOI: 10.1038/s41392-022-01039-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/16/2022] [Accepted: 05/22/2022] [Indexed: 01/18/2023] Open
Abstract
The persistent COVID-19 pandemic since 2020 has brought an enormous public health burden to the global society and is accompanied by various evolution of the virus genome. The consistently emerging SARS-CoV-2 variants harboring critical mutations impact the molecular characteristics of viral proteins and display heterogeneous behaviors in immune evasion, transmissibility, and the clinical manifestation during infection, which differ each strain and endow them with distinguished features during populational spread. Several SARS-CoV-2 variants, identified as Variants of Concern (VOC) by the World Health Organization, challenged global efforts on COVID-19 control due to the rapid worldwide spread and enhanced immune evasion from current antibodies and vaccines. Moreover, the recent Omicron variant even exacerbated the global anxiety in the continuous pandemic. Its significant evasion from current medical treatment and disease control even highlights the necessity of combinatory investigation of the mutational pattern and influence of the mutations on viral dynamics against populational immunity, which would greatly facilitate drug and vaccine development and benefit the global public health policymaking. Hence in this review, we summarized the molecular characteristics, immune evasion, and impacts of the SARS-CoV-2 variants and focused on the parallel comparison of different variants in mutational profile, transmissibility and tropism alteration, treatment effectiveness, and clinical manifestations, in order to provide a comprehensive landscape for SARS-CoV-2 variant research.
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Affiliation(s)
- Cong Sun
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Chu Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Guo-Long Bu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Lan-Yi Zhong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Department of Experimental Research, Sun Yat-sen University Cancer Center, Sun Yat-sen University, 510060, Guangzhou, China. .,Guangdong-Hong Kong Joint Laboratory for RNA Medicine, 510060, Guangzhou, China.
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Alisoltani A, Jaroszewski L, Iyer M, Iranzadeh A, Godzik A. Increased Frequency of Indels in Hypervariable Regions of SARS-CoV-2 Proteins—A Possible Signature of Adaptive Selection. Front Genet 2022; 13:875406. [PMID: 35719386 PMCID: PMC9201826 DOI: 10.3389/fgene.2022.875406] [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: 02/14/2022] [Accepted: 04/08/2022] [Indexed: 11/29/2022] Open
Abstract
Most attention in the surveillance of evolving SARS-CoV-2 genome has been centered on nucleotide substitutions in the spike glycoprotein. We show that, as the pandemic extends into its second year, the numbers and ratio of genomes with in-frame insertions and deletions (indels) increases significantly, especially among the variants of concern (VOCs). Monitoring of the SARS-CoV-2 genome evolution shows that co-occurrence (i.e., highly correlated presence) of indels, especially deletions on spike N-terminal domain and non-structural protein 6 (NSP6) is a shared feature in several VOCs such as Alpha, Beta, Delta, and Omicron. Indels distribution is correlated with spike mutations associated with immune escape and growth in the number of genomes with indels coincides with the increasing population resistance due to vaccination and previous infections. Indels occur most frequently in the spike, but also in other proteins, especially those involved in interactions with the host immune system. We also showed that indels concentrate in regions of individual SARS-CoV-2 proteins known as hypervariable regions (HVRs) that are mostly located in specific loop regions. Structural analysis suggests that indels remodel viral proteins’ surfaces at common epitopes and interaction interfaces, affecting the virus’ interactions with host proteins. We hypothesize that the increased frequency of indels, the non-random distribution of them and their independent co-occurrence in several VOCs is another mechanism of response to elevated global population immunity.
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Affiliation(s)
- Arghavan Alisoltani
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Lukasz Jaroszewski
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
| | - Mallika Iyer
- Graduate School of Biomedical Sciences, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States
| | - Arash Iranzadeh
- Computational Biology Division, Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa
| | - Adam Godzik
- Biosciences Division, School of Medicine, University of California, Riverside, Riverside, CA, United States
- *Correspondence: Adam Godzik,
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Kovacech B, Fialova L, Filipcik P, Skrabana R, Zilkova M, Paulenka-Ivanovova N, Kovac A, Palova D, Rolkova GP, Tomkova K, Csokova NT, Markova K, Skrabanova M, Sinska K, Basheer N, Majerova P, Hanes J, Parrak V, Prcina M, Cehlar O, Cente M, Piestansky J, Fresser M, Novak M, Slavikova M, Borsova K, Cabanova V, Brejova B, Vinař T, Nosek J, Klempa B, Eyer L, Hönig V, Palus M, Ruzek D, Vyhlidalova T, Strakova P, Mrazkova B, Zudova D, Koubkova G, Novosadova V, Prochazka J, Sedlacek R, Zilka N, Kontsekova E. Monoclonal antibodies targeting two immunodominant epitopes on the Spike protein neutralize emerging SARS-CoV-2 variants of concern. EBioMedicine 2022; 76:103818. [PMID: 35078012 PMCID: PMC8782626 DOI: 10.1016/j.ebiom.2022.103818] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND The emergence of new SARS-CoV-2 variants of concern B.1.1.7 (Alpha), B.1.351 (Beta), P.1 (Gamma) and B.1.617.2 (Delta) that harbor mutations in the viral S protein raised concern about activity of current vaccines and therapeutic antibodies. Independent studies have shown that mutant variants are partially or completely resistant against some of the therapeutic antibodies authorized for emergency use. METHODS We employed hybridoma technology, ELISA-based and cell-based S-ACE2 interaction assays combined with authentic virus neutralization assays to develop second-generation antibodies, which were specifically selected for their ability to neutralize the new variants of SARS-CoV-2. FINDINGS AX290 and AX677, two monoclonal antibodies with non-overlapping epitopes, exhibit subnanomolar or nanomolar affinities to the receptor binding domain of the viral Spike protein carrying amino acid substitutions N501Y, N439K, E484K, K417N, and a combination N501Y/E484K/K417N found in the circulating virus variants. The antibodies showed excellent neutralization of an authentic SARS-CoV-2 virus representing strains circulating in Europe in spring 2020 and also the variants of concern B.1.1.7 (Alpha), B.1.351 (Beta) and B.1.617.2 (Delta). In addition, AX677 is able to bind Omicron Spike protein just like the wild type Spike. The combination of the two antibodies prevented the appearance of escape mutations of the authentic SARS-CoV-2 virus. Prophylactic administration of AX290 and AX677, either individually or in combination, effectively reduced viral burden and inflammation in the lungs, and prevented disease in a mouse model of SARS-CoV-2 infection. INTERPRETATION The virus-neutralizing properties were fully reproduced in chimeric mouse-human versions of the antibodies, which may represent a promising tool for COVID-19 therapy. FUNDING The study was funded by AXON Neuroscience SE and AXON COVIDAX a.s.
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Affiliation(s)
- Branislav Kovacech
- AXON COVIDAX a. s.; Bratislava, 811 02, Slovakia; AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia.
| | - Lubica Fialova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Peter Filipcik
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Monika Zilkova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Andrej Kovac
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Denisa Palova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | | | - Natalia Turic Csokova
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Karina Markova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michaela Skrabanova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Kristina Sinska
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Neha Basheer
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Petra Majerova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Jozef Hanes
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Vojtech Parrak
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Michal Prcina
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | - Ondrej Cehlar
- Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | - Martin Cente
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
| | | | - Michal Fresser
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia
| | | | - Monika Slavikova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Kristina Borsova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia; Department of Microbiology and Virology, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Viktoria Cabanova
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Bronislava Brejova
- Department of Computer Science, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Tomas Vinař
- Department of Applied Informatics, Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava; Bratislava, 842 48, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava; Bratislava, 842 15, Slovakia
| | - Boris Klempa
- Biomedical Research Center, Institute of Virology, Slovak Academy of Sciences; Bratislava, 845 05, Slovakia
| | - Ludek Eyer
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Vaclav Hönig
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Martin Palus
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Daniel Ruzek
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic; Department of Experimental Biology, Faculty of Science, Masaryk University, Kamenice 753/5, CZ-62500 Brno, Czech Republic
| | - Tereza Vyhlidalova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic
| | - Petra Strakova
- Institute of Parasitology, Biology Centre of the Czech Academy of Sciences, Branisovska 31, CZ-37005 Ceske Budejovice, Czech Republic; Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic
| | - Blanka Mrazkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Dagmar Zudova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Gizela Koubkova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Vendula Novosadova
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Jan Prochazka
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Radislav Sedlacek
- Czech Centre of Phenogenomics, Institute of Molecular Genetics, ASCR v.v.i, Prumyslova 595, 252 50, Vestec, Czech Republic
| | - Norbert Zilka
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia.
| | - Eva Kontsekova
- AXON Neuroscience R&D Services SE; Bratislava, 811 02, Slovakia; Institute of Neuroimmunology, Slovak Academy of Sciences; Bratislava, 845 10, Slovakia
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Panzera Y, Ramos N, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Frabasile S, Fuques E, Coppola L, Goñi N, Ramas V, Sorhouet C, Bormida V, Burgueño A, Brasesco M, Garland MR, Molinari S, Perez MT, Somma R, Somma S, Morel MN, Mogdasy C, Chiparelli H, Arbiza J, Delfraro A, Pérez R. Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion. Mem Inst Oswaldo Cruz 2022; 116:e210275. [PMID: 35019072 PMCID: PMC8752050 DOI: 10.1590/0074-02760210275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
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Affiliation(s)
- Yanina Panzera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Natalia Ramos
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Lucía Calleros
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Ana Marandino
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Gonzalo Tomás
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Claudia Techera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sofía Grecco
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sandra Frabasile
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Eddie Fuques
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Leticia Coppola
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Natalia Goñi
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Viviana Ramas
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Victoria Bormida
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Analía Burgueño
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - María Brasesco
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Rosa Garland
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Sylvia Molinari
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Teresa Perez
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Rosina Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Silvana Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Noelia Morel
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cristina Mogdasy
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Héctor Chiparelli
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Juan Arbiza
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Adriana Delfraro
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Ruben Pérez
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
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8
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Bogiel T, Rzepka M, Depka D. Reliable Diagnostics of SARS-CoV-2 Infections Using One- and Two-Gene Molecular Tests for a Viral RNA Detection-Results Questioning Previous Observations. Diagnostics (Basel) 2021; 11:diagnostics11101839. [PMID: 34679537 PMCID: PMC8534906 DOI: 10.3390/diagnostics11101839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/02/2021] [Accepted: 10/03/2021] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is a new virus from the Coronaviridae family and its rapid spread is now the most important medical problem worldwide. Currently used tests vary in the number and selection of SARS-CoV-2 target genes. Meanwhile, the choice of the appropriate target gene may be important in terms of a reliable detection of a viral RNA. As some researchers questioned the sensitivity of the monogenic VIASURE SARS-CoV-2 S gene Real Time PCR Detection Kit (CerTest Biotec, Zaragoza, Spain) in mid-2020, the aim of the study was to evaluate the usefulness of this kit, used along with the BD MAX™ System (Becton Dickinson, East Rutherford, NJ, USA), and compare the results with two-gene Bosphore Novel Coronavirus (2019-nCoV) Detection Kit v1 (Anatolia Diagnostics and Biotechnology Products Inc., Istanbul, Turkey). Both tests were carried out on 306 nasopharyngeal/oropharyngeal swabs. The consistent results (72 positive and 225 negative results found simultaneously in both kits) were obtained for 297 (97.1%) samples altogether, while discrepancies between the results of the evaluated tests were observed for nine (2.9%) specimens. There were no statistically significant differences between the method used and the frequency of positive results. Both tests, targeted at detecting one and two genes, are effective in SARS-CoV-2 RNA detection.
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9
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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10
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Abstract
Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.
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11
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Panzera Y, Ramos N, Frabasile S, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Fuques E, Goñi N, Ramas V, Coppola L, Chiparelli H, Sorhouet C, Mogdasy C, Arbiza J, Delfraro A, Pérez R. A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay. Transbound Emerg Dis 2021; 68:3075-3082. [PMID: 33501730 PMCID: PMC8014828 DOI: 10.1111/tbed.14002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 01/20/2023]
Abstract
The analysis of genetic diversity in SARS‐CoV‐2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS‐CoV‐2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12‐nucleotide deletion in ORF7a, resulting in a 4‐amino acid in‐frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS‐CoV‐2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sandra Frabasile
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eddie Fuques
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Goñi
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Viviana Ramas
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Leticia Coppola
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Héctor Chiparelli
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Laboratorio de Biología Molecular, Mutualista Médica Uruguaya, Montevideo, Uruguay
| | - Cristina Mogdasy
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Adriana Delfraro
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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12
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Srivastava S, Banu S, Singh P, Sowpati DT, Mishra RK. SARS-CoV-2 genomics: An Indian perspective on sequencing viral variants. J Biosci 2021; 46:22. [PMID: 33737495 PMCID: PMC7895735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 01/25/2021] [Indexed: 04/01/2024]
Abstract
Since its emergence as a pneumonia-like outbreak in the Chinese city of Wuhan in late 2019, the novel coronavirus disease COVID-19 has spread widely to become a global pandemic. The first case of COVID-19 in India was reported on 30 January 2020 and since then it has affected more than ten million people and resulted in around 150,000 deaths in the country. Over time, the viral genome has accumulated mutations as it passes through its human hosts, a common evolutionary mechanism found in all microorganisms. This has implications for disease surveillance and management, vaccines and therapeutics, and the emergence of reinfections. Sequencing the viral genome can help monitor these changes and provides an extraordinary opportunity to understand the genetic epidemiology and evolution of the virus as well as tracking its spread in a population. Here we review the past year in the context of the phylogenetic analysis of variants isolated over the course of the pandemic in India and highlight the importance of continued sequencing-based surveillance in the country.
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Affiliation(s)
- Surabhi Srivastava
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Sofia Banu
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Priya Singh
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Divya Tej Sowpati
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
| | - Rakesh K. Mishra
- CSIR–Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, Telangana 500 007 India
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