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Almansour I, Jermy BR. Nucleic acid vaccine candidates encapsulated with mesoporous silica nanoparticles against MERS-CoV. Hum Vaccin Immunother 2024; 20:2346390. [PMID: 38691025 PMCID: PMC11067998 DOI: 10.1080/21645515.2024.2346390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/19/2024] [Indexed: 05/03/2024] Open
Abstract
Middle East respiratory coronavirus (MERS-CoV) is a newly emergent, highly pathogenic coronavirus that is associated with 34% mortality rate. MERS-CoV remains listed as priority pathogen by the WHO. Since its discovery in 2012 and despite the efforts to develop coronaviruses vaccines to fight against SARS-CoV-2, there are currently no MERS-CoV vaccine that has been approved. Therefore, there is high demand to continue on the development of prophylactic vaccines against MERS-CoV. Current advancements in vaccine developments can be adapted for the development of improved MERS-CoV vaccines candidates. Nucleic acid-based vaccines, including pDNA and mRNA, are relatively new class of vaccine platforms. In this work, we developed pDNA and mRNA vaccine candidates expressing S.FL gene of MERS-CoV. Further, we synthesized a silane functionalized hierarchical aluminosilicate to encapsulate each vaccine candidates. We tested the nucleic acid vaccine candidates in mice and evaluated humoral antibodies response. Interestingly, we determined that the non-encapsulated, codon optimized S.FL pDNA vaccine candidate elicited the highest level of antibody responses against S.FL and S1 of MERS-CoV. Encapsulation of mRNA with nanoporous aluminosilicate increased the humoral antibody responses, whereas encapsulation of pDNA did not. These findings suggests that MERS-CoV S.FL pDNA vaccine candidate induced the highest level of humoral responses. This study will enhance further optimization of nanosilica as potential carrier for mRNA vaccines. In conclusion, this study suggests MERS-CoV pDNA vaccine candidate as a suitable vaccine platform for further pivotal preclinical testings.
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Affiliation(s)
- Iman Almansour
- Nucleic Acid Vaccine Laboratory, Department of Epidemic Diseases Research, Institute for Research and Medical Consultations IRMC, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
| | - B. Rabindran Jermy
- Department of Nanomedicine Research, Institute for Research and Medical Consultations IRMC, Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia
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2
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Li W, Tahiri N. Host-Virus Cophylogenetic Trajectories: Investigating Molecular Relationships between Coronaviruses and Bat Hosts. Viruses 2024; 16:1133. [PMID: 39066295 DOI: 10.3390/v16071133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 07/10/2024] [Accepted: 07/12/2024] [Indexed: 07/28/2024] Open
Abstract
Bats, with their virus tolerance, social behaviors, and mobility, are reservoirs for emerging viruses, including coronaviruses (CoVs) known for genetic flexibility. Studying the cophylogenetic link between bats and CoVs provides vital insights into transmission dynamics and host adaptation. Prior research has yielded valuable insights into phenomena such as host switching, cospeciation, and other dynamics concerning the interaction between CoVs and bats. Nonetheless, a distinct gap exists in the current literature concerning a comparative cophylogenetic analysis focused on elucidating the contributions of sequence fragments to the co-evolution between hosts and viruses. In this study, we analyzed the cophylogenetic patterns of 69 host-virus connections. Among the 69 host-virus links examined, 47 showed significant cophylogeny based on ParaFit and PACo analyses, affirming strong associations. Focusing on two proteins, ORF1ab and spike, we conducted a comparative analysis of host and CoV phylogenies. For ORF1ab, the specific window ranged in multiple sequence alignment (positions 520-680, 770-870, 2930-3070, and 4910-5080) exhibited the lowest Robinson-Foulds (RF) distance (i.e., 84.62%), emphasizing its higher contribution in the cophylogenetic association. Similarly, within the spike region, distinct window ranges (positions 0-140, 60-180, 100-410, 360-550, and 630-730) displayed the lowest RF distance at 88.46%. Our analysis identified six recombination regions within ORF1ab (positions 360-1390, 550-1610, 680-1680, 700-1710, 2060-3090, and 2130-3250), and four within the spike protein (positions 10-510, 50-560, 170-710, and 230-730). The convergence of minimal RF distance regions with combination regions robustly affirms the pivotal role of recombination in viral adaptation to host selection pressures. Furthermore, horizontal gene transfer reveals prominent instances of partial gene transfer events, occurring not only among variants within the same host species but also crossing host species boundaries. This suggests a more intricate pattern of genetic exchange. By employing a multifaceted approach, our comprehensive strategy offers a nuanced understanding of the intricate interactions that govern the co-evolutionary dynamics between bat hosts and CoVs. This deeper insight enhances our comprehension of viral evolution and adaptation mechanisms, shedding light on the broader dynamics that propel viral diversity.
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Affiliation(s)
- Wanlin Li
- Department of Computer Science, University of Sherbrooke, 2500 Bd University, Sherbrooke, QC J1K 2R1, Canada
| | - Nadia Tahiri
- Department of Computer Science, University of Sherbrooke, 2500 Bd University, Sherbrooke, QC J1K 2R1, Canada
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3
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Polega J. The Role of Cytokines and T Cells as Mediators of Inflammatory Pathology in Type 1 Diabetes and COVID-19. Pediatr Ann 2024; 53:e264-e268. [PMID: 38949876 DOI: 10.3928/19382359-20240502-05] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 07/03/2024]
Abstract
During the coronavirus disease 2019 (COVID-19) pandemic, reports of individuals experiencing new-onset type 1 diabetes (T1D) began to appear in the literature. This spurred subsequent epidemiological studies that demonstrated an increase in new diagnosis of T1D compared to prepandemic. Development of T1D is characterized by the development of an inappropriate T cell response directed against pancreatic beta-cells, leading to eventual loss of insulin secretion. This T cell response occurs in genetically susceptible individuals and may be triggered by viral illnesses. Abnormal cytokine production is another element of the pathogenesis of T1D. Infection with severe acute respiratory syndrome related coronavirus 2 induces a profound increase in the production of inflammatory cytokines and causes significant T-cell dysregulation. These disruptions of the immune system may be linked to the development of T1D following COVID-19. [Pediatr Ann. 2024;53(7):e264-e268.].
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Kimbrell B, Huang J, Fraser A, Jiang X. Efficacy of Three Antimicrobials Against two SARS-COV-2 Surrogates, Bovine Coronavirus and Human Coronavirus OC43, on Hard or Soft Nonporous Materials. J Food Prot 2024; 87:100316. [PMID: 38878900 DOI: 10.1016/j.jfp.2024.100316] [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: 01/26/2024] [Revised: 06/07/2024] [Accepted: 06/10/2024] [Indexed: 06/25/2024]
Abstract
The efficacy of three antimicrobials was evaluated against two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surrogates - bovine coronavirus (BCoV) and human coronavirus (HCoV) OC43 - on hard and soft nonporous materials. Three antimicrobials with three different active ingredients (chlorine, hydrogen peroxide, and quaternary ammonium compound + alcohol) were studied. Initially, a neutralization method was optimized for each antimicrobial. Then, we determined their efficacy against BCoV and HCoV OC43 in both suspension and on surfaces made with polyethylene terephthalate (PET) plastic and vinyl upholstery fabric. All tests were conducted under ambient environmental conditions with a soil load of 5% fetal bovine serum. After a 2-min exposure, all three antimicrobials achieved a >3.0 log10 reduction in viral titers in suspension. All three also reduced virus infectivity on both surface materials below the detection limit (0.6 log10 TCID50/carrier). Treatments in which the reduction in virus titer was <3.0 log10 were attributed to a decreased dynamic range on the carrier during drying prior to disinfection. The carrier data revealed that both surrogates were inactivated more rapidly (p <0.05) on vinyl or under conditions of high relative humidity. Three classes of antimicrobials were efficacious against both SARS-CoV-2 surrogate viruses, with BCoV demonstrating slightly less sensitivity compared to HCoV OC43. These findings also illustrate the importance of (1) optimizing the neutralization method and (2) considering relative humidity as a key factor for efficacy testing.
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Affiliation(s)
- Breanna Kimbrell
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, USA
| | - Jinge Huang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Angela Fraser
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA
| | - Xiuping Jiang
- Department of Food, Nutrition, and Packaging Sciences, Clemson University, Clemson, South Carolina, USA.
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5
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Maio N, Heffner AL, Rouault TA. Iron‑sulfur clusters in viral proteins: Exploring their elusive nature, roles and new avenues for targeting infections. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119723. [PMID: 38599324 PMCID: PMC11139609 DOI: 10.1016/j.bbamcr.2024.119723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/13/2024] [Accepted: 04/01/2024] [Indexed: 04/12/2024]
Abstract
Viruses have evolved complex mechanisms to exploit host factors for replication and assembly. In response, host cells have developed strategies to block viruses, engaging in a continuous co-evolutionary battle. This dynamic interaction often revolves around the competition for essential resources necessary for both host cell and virus replication. Notably, iron, required for the biosynthesis of several cofactors, including iron‑sulfur (FeS) clusters, represents a critical element in the ongoing competition for resources between infectious agents and host. Although several recent studies have identified FeS cofactors at the core of virus replication machineries, our understanding of their specific roles and the cellular processes responsible for their incorporation into viral proteins remains limited. This review aims to consolidate our current knowledge of viral components that have been characterized as FeS proteins and elucidate how viruses harness these versatile cofactors to their benefit. Its objective is also to propose that viruses may depend on incorporation of FeS cofactors more extensively than is currently known. This has the potential to revolutionize our understanding of viral replication, thereby carrying significant implications for the development of strategies to target infections.
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Affiliation(s)
- Nunziata Maio
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA.
| | - Audrey L Heffner
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA; Department of Biology, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Tracey A Rouault
- Molecular Medicine Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, Bethesda, MD 20892, USA
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Sohrab SS, Alsaqaf F, Hassan AM, Tolah AM, Bajrai LH, Azhar EI. Genomic Diversity and Recombination Analysis of the Spike Protein Gene from Selected Human Coronaviruses. BIOLOGY 2024; 13:282. [PMID: 38666894 PMCID: PMC11048170 DOI: 10.3390/biology13040282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 04/28/2024]
Abstract
Human coronaviruses (HCoVs) are seriously associated with respiratory diseases in humans and animals. The first human pathogenic SARS-CoV emerged in 2002-2003. The second was MERS-CoV, reported from Jeddah, the Kingdom of Saudi Arabia, in 2012, and the third one was SARS-CoV-2, identified from Wuhan City, China, in late December 2019. The HCoV-Spike (S) gene has the highest mutation/insertion/deletion rate and has been the most utilized target for vaccine/antiviral development. In this manuscript, we discuss the genetic diversity, phylogenetic relationships, and recombination patterns of selected HCoVs with emphasis on the S protein gene of MERS-CoV and SARS-CoV-2 to elucidate the possible emergence of new variants/strains of coronavirus in the near future. The findings showed that MERS-CoV and SARS-CoV-2 have significant sequence identity with the selected HCoVs. The phylogenetic tree analysis formed a separate cluster for each HCoV. The recombination pattern analysis showed that the HCoV-NL63-Japan was a probable recombinant. The HCoV-NL63-USA was identified as a major parent while the HCoV-NL63-Netherland was identified as a minor parent. The recombination breakpoints start in the viral genome at the 142 nucleotide position and end at the 1082 nucleotide position with a 99% CI and Bonferroni-corrected p-value of 0.05. The findings of this study provide insightful information about HCoV-S gene diversity, recombination, and evolutionary patterns. Based on these data, it can be concluded that the possible emergence of new strains/variants of HCoV is imminent.
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Affiliation(s)
- Sayed Sartaj Sohrab
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Fatima Alsaqaf
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Mohamed Hassan
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
| | - Ahmed Majdi Tolah
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Science, King Abdulaziz University, P.O. Box 21911, Rabigh 344, Saudi Arabia
| | - Leena Hussein Bajrai
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Biochemistry Department, Faculty of Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
| | - Esam Ibraheem Azhar
- Special Infectious Agents Unit, King Fahd Medical Research Center, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia; (F.A.); (A.M.H.); (A.M.T.); (L.H.B.)
- Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, P.O. Box 80216, Jeddah 21589, Saudi Arabia
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7
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Sopjani M, Falco F, Impellitteri F, Guarrasi V, Nguyen Thi X, Dërmaku-Sopjani M, Faggio C. Flavonoids derived from medicinal plants as a COVID-19 treatment. Phytother Res 2024; 38:1589-1609. [PMID: 38284138 DOI: 10.1002/ptr.8123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 11/30/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes COVID-19 disease. Through its viral spike (S) protein, the virus enters and infects epithelial cells by utilizing angiotensin-converting enzyme 2 as a host cell's receptor protein. The COVID-19 pandemic had a profound impact on global public health and economies. Although various effective vaccinations and medications are now available to prevent and treat COVID-19, natural compounds derived from medicinal plants, particularly flavonoids, demonstrated therapeutic potential to treat COVID-19 disease. Flavonoids exhibit dual antiviral mechanisms: direct interference with viral invasion and inhibition of replication. Specifically, they target key viral molecules, particularly viral proteases, involved in infection. These compounds showcase significant immunomodulatory and anti-inflammatory properties, effectively inhibiting various inflammatory cytokines. Additionally, emerging evidence supports the potential of flavonoids to mitigate the progression of COVID-19 in individuals with obesity by positively influencing lipid metabolism. This review aims to elucidate the molecular structure of SARS-CoV-2 and the underlying mechanism of action of flavonoids on the virus. This study evaluates the potential anti-SARS-CoV-2 properties exhibited by flavonoid compounds, with a specific interest in their structure and mechanisms of action, as therapeutic applications for the prevention and treatment of COVID-19. Nevertheless, a significant portion of existing knowledge is based on theoretical frameworks and findings derived from in vitro investigations. Further research is required to better assess the effectiveness of flavonoids in combating SARS-CoV-2, with a particular emphasis on in vivo and clinical investigations.
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Affiliation(s)
- Mentor Sopjani
- Faculty of Medicine, University of Prishtina, Prishtina, Kosova
| | - Francesca Falco
- Institute for Marine Biological Resources and Biotechnology (IRBIM)-CNR, Mazara del Vallo, Italy
| | | | - Valeria Guarrasi
- Institute of Biophysics, National Research Council (CNR), Palermo, Italy
| | - Xuan Nguyen Thi
- Institute of Genome Research, Vietnam Academy of Science and Technology, Hanoi, Vietnam
| | | | - Caterina Faggio
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Messina, Italy
- Department of Eco sustainable Marine Biotechnology, Stazione Zoologica Anton Dohrn, Naples, Italy
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Xia T, Xu S, Li X, Ruan W. Avian coronavirus infectious bronchitis virus Beaudette strain NSP9 interacts with STAT1 and inhibits its phosphorylation to facilitate viral replication. Virology 2024; 590:109944. [PMID: 38141500 DOI: 10.1016/j.virol.2023.109944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 11/11/2023] [Accepted: 11/16/2023] [Indexed: 12/25/2023]
Abstract
Avian coronavirus, known as infectious bronchitis virus (IBV), is the causative agent of infectious bronchitis (IB). Viral nonstructural proteins play important roles in viral replication and immune modulation. IBV NSP9 is a component of the RNA replication complex for viral replication. In this study, we uncovered a function of NSP9 in immune regulation. First, the host proteins that interacted with NSP9 were screened. The immune-related protein signal transducer and activator of transcription 1 (STAT1) was identified and the interaction between NSP9 and STAT1 was further confirmed. Furthermore, IBV replication was inhibited in STAT1-overexpressing cells but inversely affected in STAT1 knock-down cells. Importantly, NSP9 inhibited STAT1 phosphorylation. Finally, the expression of JAK/STAT pathway downstream genes IRF7 and ISG20 was significantly decreased in NSP9-overexpressing cells. These results showed the important role of IBV NSP9 in immunosuppression.
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Affiliation(s)
- Ting Xia
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Shengkui Xu
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Xueyan Li
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Wenke Ruan
- College of Animal Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.
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9
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [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: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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Pipek OA, Medgyes-Horváth A, Stéger J, Papp K, Visontai D, Koopmans M, Nieuwenhuijse D, Oude Munnink BB, Csabai I. Systematic detection of co-infection and intra-host recombination in more than 2 million global SARS-CoV-2 samples. Nat Commun 2024; 15:517. [PMID: 38225254 PMCID: PMC10789779 DOI: 10.1038/s41467-023-43391-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 11/06/2023] [Indexed: 01/17/2024] Open
Abstract
Systematic monitoring of SARS-CoV-2 co-infections between different lineages and assessing the risk of intra-host recombinant emergence are crucial for forecasting viral evolution. Here we present a comprehensive analysis of more than 2 million SARS-CoV-2 raw read datasets submitted to the European COVID-19 Data Portal to identify co-infections and intra-host recombination. Co-infection was observed in 0.35% of the investigated cases. Two independent procedures were implemented to detect intra-host recombination. We show that sensitivity is predominantly determined by the density of lineage-defining mutations along the genome, thus we used an expanded list of mutually exclusive defining mutations of specific variant combinations to increase statistical power. We call attention to multiple challenges rendering recombinant detection difficult and provide guidelines for the reduction of false positives arising from chimeric sequences produced during PCR amplification. Additionally, we identify three recombination hotspots of Delta - Omicron BA.1 intra-host recombinants.
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Affiliation(s)
- Orsolya Anna Pipek
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Anna Medgyes-Horváth
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary.
| | - József Stéger
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Krisztián Papp
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Dávid Visontai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
| | - Marion Koopmans
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - David Nieuwenhuijse
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus University Medical Center, Rotterdam, Netherlands
| | - István Csabai
- Department of Physics of Complex Systems, ELTE Eötvös Loránd University, Pázmány P. s. 1A, Budapest, 1117, Hungary
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11
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nat Biotechnol 2024; 42:139-147. [PMID: 37081138 PMCID: PMC10791578 DOI: 10.1038/s41587-023-01753-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 03/16/2023] [Indexed: 04/22/2023]
Abstract
Current methods for inference of phylogenetic trees require running complex pipelines at substantial computational and labor costs, with additional constraints in sequencing coverage, assembly and annotation quality, especially for large datasets. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes and bypasses traditional steps in phylogeny inference, such as genome assembly, annotation and all-versus-all sequence comparisons, while retaining accuracy. In a benchmark encompassing a broad variety of datasets, Read2Tree is 10-100 times faster than assembly-based approaches and in most cases more accurate-the exception being when sequencing coverage is high and reference species very distant. Here, to illustrate the broad applicability of the tool, we reconstruct a yeast tree of life of 435 species spanning 590 million years of evolution. We also apply Read2Tree to >10,000 Coronaviridae samples, accurately classifying highly diverse animal samples and near-identical severe acute respiratory syndrome coronavirus 2 sequences on a single tree. The speed, accuracy and versatility of Read2Tree enable comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Computer Science, ETH, Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.
- Department of Computer Science, Rice University, Houston, TX, USA.
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.
- Department of Computer Science, University College London, London, UK.
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London, UK.
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Chaudhury S, Kaur P, Gupta D, Anand P, Chaudhary M, Tiwari S, Mittal A, Gupta J, Kaur S, Singh VD, Dhawan D, Singh P, Sahu SK. Therapeutic Management with Repurposing Approaches: A Mystery During COVID-19 Outbreak. Curr Mol Med 2024; 24:712-733. [PMID: 37312440 DOI: 10.2174/1566524023666230613141746] [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: 08/31/2022] [Revised: 02/10/2023] [Accepted: 02/13/2023] [Indexed: 06/15/2023]
Abstract
The ubiquitous pandemic that emerged due to COVID-19 affected the whole planet. People all over the globe became vulnerable to the unpredictable emergence of coronavirus. The sudden emergence of respiratory disease in coronavirus infected several patients. This affected human life drastically, from mild symptoms to severe illness, leading to mortality. COVID-19 is an exceptionally communicable disease caused by SARS-CoV-2. According to a genomic study, the viral spike RBD interactions with the host ACE2 protein from several coronavirus strains and the interaction between RBD and ACE2 highlighted the potential change in affinity from the virus causing the COVID-19 outbreak to a progenitor type of SARS-CoV-2. SARS-CoV-2, which could be the principal reservoir, is phylogenetically related to the SARS-like bat virus. Other research works reported that intermediary hosts for the transmission of viruses to humans could include cats, bats, snakes, pigs, ferrets, orangutans, and monkeys. Even with the arrival of vaccines and individuals getting vaccinated and treated with FDAapproved repurposed drugs like Remdesivir, the first and foremost steps aimed towards the possible control and minimization of community transmission of the virus include social distancing, self-realization, and self-health care. In this review paper, we discussed and summarized various approaches and methodologies adopted and proposed by researchers all over the globe to help with the management of this zoonotic outbreak by following repurposed approaches.
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Affiliation(s)
- Soumik Chaudhury
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Paranjeet Kaur
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Deepali Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Palak Anand
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Manish Chaudhary
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Siddhita Tiwari
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Amit Mittal
- Faculty of Pharmaceutical Sciences, Desh Bhagat University, Amloh Road, Mandi Gobindgarh, 147301, Punjab, India
| | - Jeena Gupta
- School of Bioscience, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sukhmeen Kaur
- Department of Opthalmology, Punjab Institute of Medical Sciences, Jalandhar, 144001, Punjab, India
| | - Varsh Deep Singh
- American University of Barbados, Wildey, St. Michael, BB11100, Barbados
| | - Dakshita Dhawan
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Princejyot Singh
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
| | - Sanjeev Kumar Sahu
- School of Pharmaceutical Sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, 144411, Punjab, India
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13
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Queirós-Reis L, Mesquita JR, Brancale A, Bassetto M. Exploring the Fatty Acid Binding Pocket in the SARS-CoV-2 Spike Protein - Confirmed and Potential Ligands. J Chem Inf Model 2023; 63:7282-7298. [PMID: 37991468 DOI: 10.1021/acs.jcim.3c00803] [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: 11/23/2023]
Abstract
Severe Acute Respiratory syndrome 2 (SARS-CoV-2) is a respiratory virus responsible for coronavirus disease 19 (COVID-19) and the still ongoing and unprecedented global pandemic. The key viral protein for cell infection is the spike glycoprotein, a surface-exposed fusion protein that both recognizes and mediates entry into host cells. Within the spike glycoprotein, a fatty acid binding pocket (FABP) was confirmed, with the crystallization of linoleic acid (LA) occupying a well-defined site. Importantly, when the pocket is occupied by a fatty acid, an inactive conformation is stabilized, and cell recognition is hindered. In this review, we discuss ligands reported so far for this site, correlating their activity predicted through in silico studies with antispike experimental activity, assessed by either binding assays or cell-infection assays. LA was the first confirmed ligand, cocrystallized in a cryo-EM structure of the spike protein, resulting in increased stability of the inactive conformation of the spike protein. The next identified ligand, lifitegrast, was also experimentally confirmed as a ligand with antiviral activity, suggesting the potential for diverse chemical scaffolds to bind this site. Finally, SPC-14 was also confirmed as a ligand, although no inhibition assays were performed. In this review, we identified 20 studies describing small-molecule compounds predicted to bind the pocket in in silico studies and with confirmed binding or in vitro activity, either inhibitory activity against the spike-ACE2 interaction or antiviral activity in cell-based assays. When considering all ligands confirmed with in vitro assays, a good overall occupation of the pocket should be complemented with the ability to make direct interactions, both hydrophilic and hydrophobic, with key amino acid residues defining the pocket surface. Among the active compounds, long flexible carbon chains are recurrent, with retinoids capable of binding the FABP, although bulkier systems are also capable of affecting viral fitness. Compounds able to bind this site with high affinity have the potential to stabilize the inactive conformation of the SARS-CoV-2 spike protein and therefore reduce the virus's ability to infect new cells. Since this pocket is conserved in highly pathogenic human coronaviruses, including MERS-CoV and SARS-CoV, this effect could be exploited for the development of new antiviral agents, with broad-spectrum anticoronavirus activity.
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Affiliation(s)
- Luís Queirós-Reis
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
| | - João R Mesquita
- Abel Salazar Institute of Biomedical Sciences (ICBAS), University of Porto, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4050-091 Porto, Portugal
| | - Andrea Brancale
- University of Chemistry and Technology, Prague, 166 28 Praha, Czechia
| | - Marcella Bassetto
- School of Pharmacy and Pharmaceutical Sciences, College of Biomedical and Life Sciences, Cardiff University, Cardiff CF10 3BN, U.K
- Department of Chemistry, Faculty of Science and Engineering, Swansea University, Swansea SA2 8PP, U.K
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14
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Ng JPL, Xiao Yun Y, Adnan Nasim A, Gianoncelli A, Yuan Kwan Law B, Ribaudo G, Kam Wai Wong V, Coghi P. Synthesis, docking studies and biological evaluation of 1H-1,2,3-triazole-7-chloroquinoline derivatives against SARS-CoV-2. Bioorg Chem 2023; 141:106882. [PMID: 37839144 DOI: 10.1016/j.bioorg.2023.106882] [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: 08/02/2023] [Revised: 09/12/2023] [Accepted: 09/22/2023] [Indexed: 10/17/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a single-stranded enveloped positive RNA virus and the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Chloroquine (CQ), an antimalarial drug, was reported to be active against several viruses including coronaviruses. The mechanism of host cell invasion by SARS-CoV-2 involves the interaction of angiotensin-converting enzyme (ACE2) with receptor-binding domain (RBD) of spike protein (S). The main protease (Mpro/3CLpro) is an attractive drug target due to its vital function in regulation of polyprotein translated from viral RNA. In this study, a series of novel quinoline-triazole hybrid compounds was synthesized and subjected to evaluations on their cytotoxicity, interactions with different variants of RBD in SARS-CoV-2 and with 3CLpro enzyme by experimental and computational techniques to identify their ability of counteracting viral infection. The results of bio-layer interferometry showed that quinoline derivative 11 has good interaction with delta plus and omicron RBD variants (KD = 3.46 × 10-5 and 6.38 × 10-5 M) while derivative 1 is the best binder for recent variant omicron (KD = 26.9 µM) among the series. Potent compounds 1-4 and 11 also demonstrated a suppressive effect on 3CLpro activity in a non-dose-dependent manner. Further docking study revealed that these compounds interacted within the same area of RBD, while no correlation was found for 3CLpro. Furthermore, the molecular dynamics simulations were carried out to assess the conformational stability of docked complexes for preliminary verification.
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Affiliation(s)
- Jerome P L Ng
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Yun Xiao Yun
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ali Adnan Nasim
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Alessandra Gianoncelli
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy
| | - Betty Yuan Kwan Law
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, University of Brescia, Brescia, Italy.
| | - Vincent Kam Wai Wong
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
| | - Paolo Coghi
- Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; School of Pharmacy, Macau University of Science and Technology, Macau, China.
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15
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Fan Y, Hou Y, Li Q, Dian Z, Wang B, Xia X. RNA virus diversity in rodents. Arch Microbiol 2023; 206:9. [PMID: 38038743 DOI: 10.1007/s00203-023-03732-4] [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: 09/07/2023] [Revised: 11/01/2023] [Accepted: 11/02/2023] [Indexed: 12/02/2023]
Abstract
Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.
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Affiliation(s)
- Yayu Fan
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Yutong Hou
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Qian Li
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, Kunming, Yunnan, 650032, People's Republic of China
| | - Binghui Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
| | - Xueshan Xia
- Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming, Yunnan, 650500, People's Republic of China.
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16
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Hu GM, Tai YC, Chen CM. Unraveling the evolutionary patterns and phylogenomics of coronaviruses: A consensus network approach. J Med Virol 2023; 95:e29233. [PMID: 38009694 DOI: 10.1002/jmv.29233] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/19/2023] [Accepted: 10/31/2023] [Indexed: 11/29/2023]
Abstract
The COVID-19 pandemic emphasizes the significance of studying coronaviruses (CoVs). This study investigates the evolutionary patterns of 350 CoVs using four structural proteins (S, E, M, and N) and introduces a consensus methodology to construct a comprehensive phylogenomic network. Our clustering of CoVs into 4 genera is consistent with the current CoV classification. Additionally, we calculate network centrality measures to identify CoV strains with significant average weighted degree and betweenness centrality values, with a specific focus on RaTG13 in the beta genus and NGA/A116E7/2006 in the gamma genus. We compare the phylogenetics of CoVs using our distance-based approach and the character-based model with IQ-TREE. Both methods yield largely consistent outcomes, indicating the reliability of our consensus approach. However, it is worth mentioning that our consensus method achieves an approximate 5000-fold increase in speed compared to IQ-TREE when analyzing the data set of 350 CoVs. This improved efficiency enhances the feasibility of conducting large-scale phylogenomic studies on CoVs.
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Affiliation(s)
- Geng-Ming Hu
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Yu-Chen Tai
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
| | - Chi-Ming Chen
- Department of Physics, National Taiwan Normal University, Taipei, Taiwan
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17
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Krentz D, Bergmann M, Felten S, Hartmann K. [Options for treatment of feline infectious peritonitis - previously and today]. TIERARZTLICHE PRAXIS. AUSGABE K, KLEINTIERE/HEIMTIERE 2023; 51:351-360.. [PMID: 37956666 DOI: 10.1055/a-2147-3999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Feline infectious peritonitis (FIP) is one of the most common infectious diseases in cats that is fatal when untreated. So far, there is no legally available effective treatment in Germany. Treatment options include only symptomatic treatment (e. g. glucocorticoids, propentofylline), immunomodulatory approaches (e. g. interferons, polyprenyl immunostimulant), and antiviral chemotherapy with protease inhibitors (e. g. GC376) or nucleoside analogues (e. g. GS-441524, remdesivir). Symptomatic treatment does not cure FIP but may lead to a short-term improvement of clinical signs in a subset of cats. Immunomodulatory treatment has also not shown to be very promising. In contrary, the antiviral compounds GS-441524 and GC376 exhibited significant efficacy in several studies and their use saved the lives of many cats suffering from FIP. However, both agents are currently not licensed and thus cannot be legally administered by veterinarians in Germany. Legally, cats may only be legally treated with GS-441524 in a few countries (e.g. Great Britain and Australia). In other countries, GS-441524 is imported by cat owners via the black market and administered on their own. This article provides an overview of the available treatment options and an outlook on the legal use of effective antiviral drugs.
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Affiliation(s)
- Daniela Krentz
- Medizinische Kleintierklinik der Ludwig-Maximilians-Universität München
| | - Michèle Bergmann
- Medizinische Kleintierklinik der Ludwig-Maximilians-Universität München
| | - Sandra Felten
- Medizinische Kleintierklinik der Ludwig-Maximilians-Universität München
| | - Katrin Hartmann
- Medizinische Kleintierklinik der Ludwig-Maximilians-Universität München
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18
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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19
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George U, George O, Oguzie J, Osasona O, Motayo B, Kamani J, Eromon P, Folarin O, Happi A, Komolafe I, Happi C. Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria. Virus Res 2023; 334:199174. [PMID: 37467933 PMCID: PMC10392604 DOI: 10.1016/j.virusres.2023.199174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/12/2023] [Accepted: 07/15/2023] [Indexed: 07/21/2023]
Abstract
Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.
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Affiliation(s)
- Uwem George
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | | | - Judith Oguzie
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Oluwadamilola Osasona
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Babatunde Motayo
- Department of Medical Microbiology, Federal Medical Centre, Abeokuta, Nigeria
| | - Joshua Kamani
- Parasitology Division National Veterinary Research Institute NVRI PMB 01, Vom, Plateau state Nigeria
| | - Philomena Eromon
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Onikepe Folarin
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Anise Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria
| | - Isaac Komolafe
- Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria
| | - Christian Happi
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Osun State, Nigeria; Department of Biological Sciences, Faculty of Natural Sciences, Redeemer's University, Ede, Osun State, Nigeria.
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20
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Kaur R, Tada T, Landau NR. Restriction of SARS-CoV-2 replication by receptor transporter protein 4 (RTP4). mBio 2023; 14:e0109023. [PMID: 37382452 PMCID: PMC10470548 DOI: 10.1128/mbio.01090-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 05/09/2023] [Indexed: 06/30/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is subject to restriction by several interferon-inducible host proteins. To identify novel factors that limit replication of the virus, we tested a panel of genes that we found were induced by interferon treatment of primary human monocytes by RNA sequencing. Further analysis showed that one of the several candidates genes tested, receptor transporter protein 4 (RTP4), that had previously been shown to restrict flavivirus replication, prevented the replication of the human coronavirus HCoV-OC43. Human RTP4 blocked the replication of SARS-CoV-2 in susceptible ACE2.CHME3 cells and was active against SARS-CoV-2 Omicron variants. The protein prevented the synthesis of viral RNA, resulting in the absence of detectable viral protein synthesis. RTP4 bound the viral genomic RNA and the binding was dependent on the conserved zinc fingers in the amino-terminal domain. Expression of the protein was strongly induced in SARS-CoV-2-infected mice although the mouse homolog was inactive against the virus, suggesting that the protein is active against another virus that remains to be identified. IMPORTANCE The rapid spread of a pathogen of human coronavirus (HCoV) family member, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), around the world has led to a coronavirus disease 2019 (COVID-19) pandemic. The COVID-19 pandemic spread highlights the need for rapid identification of new broad-spectrum anti-coronavirus drugs and screening of antiviral host factors capable of inhibiting coronavirus infection. In the present work, we identify and characterize receptor transporter protein 4 (RTP4) as a host restriction factor that restricts coronavirus infection. We examined the antiviral role of hRTP4 toward the coronavirus family members including HCoV-OC43, SARS-CoV-2, Omicron BA.1, and BA.2. Molecular and biochemical analysis showed that hRTP4 binds to the viral RNA and targets the replication phase of viral infection and is associated with reduction of nucleocapsid protein. Significant higher levels of ISGs were observed in SARS-CoV-2 mouse model, suggesting the role of RTP4 in innate immune regulation in coronavirus infection. The identification of RTP4 reveals a potential target for therapy against coronavirus infection.
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Affiliation(s)
- Ramanjit Kaur
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Takuya Tada
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
| | - Nathaniel Roy Landau
- Department of Microbiology, NYU Grossman School of Medicine, New York, New York, USA
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21
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He WT, Li D, Baele G, Zhao J, Jiang Z, Ji X, Veit M, Suchard MA, Holmes EC, Lemey P, Boni MF, Su S. Newly identified lineages of porcine hemagglutinating encephalomyelitis virus exhibit respiratory phenotype. Virus Evol 2023; 9:vead051. [PMID: 37711483 PMCID: PMC10499004 DOI: 10.1093/ve/vead051] [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: 01/04/2023] [Revised: 05/18/2023] [Accepted: 08/13/2023] [Indexed: 09/16/2023] Open
Abstract
Swine pathogens have a long history of zoonotic transmission to humans, occasionally leading to sustained outbreaks or pandemics. Through a retrospective epidemiological study of swine populations in China, we describe novel lineages of porcine hemagglutinating encephalomyelitis virus (PHEV) complex coronaviruses (CoVs) that cause exclusively respiratory symptoms with no signs of the neurological symptoms typically associated with classical PHEV infection. Through large-scale epidemiological surveillance, we show that these novel lineages have circulated in at least eight provinces in southeastern China. Phylogenetic and recombination analyses of twenty-four genomes identified two major viral lineages causing respiratory symptoms with extensive recombination within them, between them, and between classical PHEV and the novel respiratory variant PHEV (rvPHEV) lineages. Divergence times among the sampled lineages in the PHEV virus complex date back to 1886-1958 (mean estimate 1928), with the two major rvPHEV lineages separating approximately 20 years later. Many rvPHEV viruses show amino acid substitutions at the carbohydrate-binding site of hemagglutinin esterase (HE) and/or have lost the cysteine required for HE dimerization. This resembles the early adaptation of human CoVs, where HE lost its hemagglutination ability to adapt to growth in the human respiratory tract. Our study represents the first report of the evolutionary history of rvPHEV circulating in swine and highlights the importance of characterizing CoV diversity and recombination in swine to identify pathogens with outbreak potential that could threaten swine farming.
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Affiliation(s)
- Wan-Ting He
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Dongyan Li
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | - Jin Zhao
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhiwen Jiang
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiang Ji
- Department of Mathematics, School of Science & Engineering, Tulane University, New Orleans, LA 70118, USA
| | - Michael Veit
- Institute for Virology, Center for Infection Medicine, Veterinary Faculty, Free University Berlin, Berlin 14163, Germany
| | - Marc A Suchard
- Department of Biostatistics, Fielding School of Public Health, and Departments of Biomathematics and Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Edward C Holmes
- Sydney Institute for Infectious Diseases, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory for Clinical and Epidemiological Virology, KU Leuven, Leuven 3000, Belgium
| | | | - Shuo Su
- Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing 210095, China
- Center for Infectious Disease Dynamics, Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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22
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Italiya J, Vacek V, Matějů P, Dering C, Celina SS, Ndiaye A, Černý J. First Detection of SARS-CoV-2 in White Rhinoceros during a Small-Scale Coronavirus Surveillance in the Bandia Reserve, Senegal. Animals (Basel) 2023; 13:2593. [PMID: 37627384 PMCID: PMC10451883 DOI: 10.3390/ani13162593] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/25/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
The SARS-CoV-2 pandemic has heightened interest in the monitoring and surveillance of coronaviruses in wildlife. Testing for the virus in animals can provide valuable insights into viral reservoirs, transmission, and pathogenesis. In this study, we present the results of the molecular surveillance project focused on coronaviruses in Senegalese wildlife. During the project, we screened fecal samples of the wild animals living in the Bandia Reserve (ten non-human primates, one giraffe, and two white rhinoceros) and the free-living urban population of African four-toed hedgehogs in Ngaparou. The results showed the absence of coronaviruses in hedgehogs, non-human primates, and a giraffe. A single positive sample was obtained from a white rhinoceros. The sequencing results of amplified RdRp gene confirmed that the detected virus was SARS-CoV-2. This study represents the first documented instance of molecular detection of SARS-CoV-2 in white rhinoceros and, therefore, extends our knowledge of possible SARS-CoV-2 hosts.
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Affiliation(s)
- Jignesh Italiya
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
| | - Vojtěch Vacek
- Department of Zoology and Fisheries, Faculty of Agrobiology, Food, and Natural Resources, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | - Petr Matějů
- Department of Animal Science and Food Processing, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic;
| | | | - Seyma S. Celina
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
| | - Arame Ndiaye
- Centre d’Études pour la Génétique et la Conservation (CEGEC S.A.S.U.), Dakar 10455, Senegal;
| | - Jiří Černý
- Center for Infectious Animal Diseases, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, 165 00 Prague, Czech Republic (J.Č.)
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23
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François S, Nazki S, Vickers SH, Fournié G, Perrins CM, Broadbent AJ, Pybus OG, Hill SC. Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild. J Gen Virol 2023; 104. [PMID: 37589541 DOI: 10.1099/jgv.0.001883] [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] [Indexed: 08/18/2023] Open
Abstract
Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.
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Affiliation(s)
- Sarah François
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
| | - Salik Nazki
- Pandemic Sciences Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Headington, Oxford, OX3 7FZ, UK
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
| | - Stephen H Vickers
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Guillaume Fournié
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Gènes-Champanelle, France
| | | | - Andrew J Broadbent
- The Pirbright Institute, Ash Rd, Pirbright, Woking GU24 0NF, UK
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD20742, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, South Park Road, Oxford, OX1 3SY, UK
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
| | - Sarah C Hill
- Department of Pathobiology and Population Science, Royal Veterinary College, Hawkshead Lane, Hatfield, AL9 7TA, UK
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24
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Hemnani M, Silva PGD, Thompson G, Poeta P, Rebelo H, Mesquita JR. First Report of Alphacoronavirus Circulating in Cavernicolous Bats from Portugal. Viruses 2023; 15:1521. [PMID: 37515207 PMCID: PMC10384150 DOI: 10.3390/v15071521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 07/03/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
The emergence of novel coronaviruses (CoVs) has emphasized the need to understand their diversity and distribution in animal populations. Bats have been identified as crucial reservoirs for CoVs, and they are found in various bat species worldwide. In this study, we investigated the presence of CoVs of four cavernicolous bats in six locations in the centre and south of Portugal. We collected faeces, anal, and buccal swab samples, as well as air samples from the locations using a Coriolis air sampler. Our results indicate that CoVs were more readily detected in faecal samples compared to anal and buccal swab samples. No CoVs were detected in the air samples. Phylogenetic analysis showed that the detected viruses belong to the Alphacoronavirus genus. This study represents the first report of Alphacoronaviruses circulating in bats in Portugal and highlights the importance of continuous surveillance for novel CoVs in bat populations globally. Ongoing surveillance for CoVs in bat populations is essential as they are a vital source of these viruses. It is crucial to understand the ecological relationships between animals, humans, and the environment to prevent and control the emergence and transmission of infectious diseases. Further ecological studies are needed to investigate the factors contributing to the emergence and transmission of zoonotic viruses.
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Affiliation(s)
- Mahima Hemnani
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
| | - Priscilla Gomes da Silva
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
- Laboratório Para a Investigação Integrativa e Translacional em Saúde Populacional (ITR), 4050-313 Porto, Portugal
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnotlogy and Energy, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
- ALiCE-Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4099-002 Porto, Portugal
| | - Gertrude Thompson
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisbon, 1099-085 Caparica, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre, Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Hugo Rebelo
- Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Universidade do Porto, 4485-661 Vairão, Portugal
- ESS, Instituto Politécnico de Setúbal, 2910-761 Setúbal, Portugal
| | - João R Mesquita
- School of Medicine and Biomedical Sciences, Porto University, 4050-313 Porto, Portugal
- Epidemiology Research Unit (EPIunit), Institute of Public Health, University of Porto, 4099-002 Porto, Portugal
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25
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Wells HL, Bonavita CM, Navarrete-Macias I, Vilchez B, Rasmussen AL, Anthony SJ. The coronavirus recombination pathway. Cell Host Microbe 2023; 31:874-889. [PMID: 37321171 PMCID: PMC10265781 DOI: 10.1016/j.chom.2023.05.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 06/17/2023]
Abstract
Recombination is thought to be a mechanism that facilitates cross-species transmission in coronaviruses, thus acting as a driver of coronavirus spillover and emergence. Despite its significance, the mechanism of recombination is poorly understood, limiting our potential to estimate the risk of novel recombinant coronaviruses emerging in the future. As a tool for understanding recombination, here, we outline a framework of the recombination pathway for coronaviruses. We review existing literature on coronavirus recombination, including comparisons of naturally observed recombinant genomes as well as in vitro experiments, and place the findings into the recombination pathway framework. We highlight gaps in our understanding of coronavirus recombination illustrated by the framework and outline how further experimental research is critical for disentangling the molecular mechanism of recombination from external environmental pressures. Finally, we describe how an increased understanding of the mechanism of recombination can inform pandemic predictive intelligence, with a retrospective emphasis on SARS-CoV-2.
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Affiliation(s)
- Heather L Wells
- Department of Ecology, Evolution, and Environmental Biology, Columbia University, New York, NY, USA; Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
| | - Cassandra M Bonavita
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Isamara Navarrete-Macias
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Blake Vilchez
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA
| | - Angela L Rasmussen
- Vaccine and Infectious Disease Organization, University of Saskatchewan, Saskatoon, SK, Canada
| | - Simon J Anthony
- Department of Pathology, Microbiology, and Immunology, University of California Davis School of Veterinary Medicine, Davis, CA, USA.
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26
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Li F, Fang T, Guo F, Zhao Z, Zhang J. Comprehensive Understanding of the Kinetic Behaviors of Main Protease from SARS-CoV-2 and SARS-CoV: New Data and Comparison to Published Parameters. Molecules 2023; 28:4605. [PMID: 37375160 DOI: 10.3390/molecules28124605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Revised: 05/15/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
The main protease (Mpro) is a promising drug target for inhibiting the coronavirus due to its conserved properties and lack of homologous genes in humans. However, previous studies on Mpro's kinetic parameters have been confusing, hindering the selection of accurate inhibitors. Therefore, obtaining a clear view of Mpro's kinetic parameters is necessary. In our study, we investigated the kinetic behaviors of Mpro from SARS-CoV-2 and SARS-CoV using both FRET-based cleavage assay and the LC-MS method, respectively. Our findings indicate that the FRET-based cleavage assay could be used for preliminary screening of Mpro inhibitors, while the LC-MS method should be applied to select the effective inhibitors with higher reliability. Furthermore, we constructed the active site mutants (H41A and C145A) and measured the kinetic parameters to gain a deeper understanding of the atomic-level enzyme efficiency reduction compared to the wild type. Overall, our study provides valuable insights for inhibitor screening and design by offering a comprehensive understanding of Mpro's kinetic behaviors.
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Affiliation(s)
- Fangya Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Tingting Fang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Feng Guo
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Zipeng Zhao
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Jianyu Zhang
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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27
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Su M, Zheng G, Xu X, Song H. Antigen epitopes of animal coronaviruses: a mini-review. ANIMAL DISEASES 2023; 3:14. [PMID: 37220551 PMCID: PMC10189233 DOI: 10.1186/s44149-023-00080-0] [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: 02/16/2023] [Accepted: 04/13/2023] [Indexed: 05/25/2023] Open
Abstract
Coronaviruses are widespread in nature and can infect mammals and poultry, making them a public health concern. Globally, prevention and control of emerging and re-emerging animal coronaviruses is a great challenge. The mechanisms of virus-mediated immune responses have important implications for research on virus prevention and control. The antigenic epitope is a chemical group capable of stimulating the production of antibodies or sensitized lymphocytes, playing an important role in antiviral immune responses. Thus, it can shed light on the development of diagnostic methods and novel vaccines. Here, we have reviewed advances in animal coronavirus antigenic epitope research, aiming to provide a reference for the prevention and control of animal and human coronaviruses. Supplementary Information The online version contains supplementary material available at 10.1186/s44149-023-00080-0.
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Affiliation(s)
- Mingjun Su
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Guanghui Zheng
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Xiangwen Xu
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
| | - Houhui Song
- Key Laboratory of Applied Technology On Green-Eco-Healthy Animal Husbandry of Zhejiang Province, Zhejiang Provincial Engineering Research Center for Animal Health Diagnostics & Advanced Technology, Zhejiang International Science and Technology Cooperation Base for Veterinary Medicine and Health Management, China-Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology & College of Veterinary Medicine of Zhejiang, A&F University, 666 Wusu Street, Lin’an District, Hangzhou, 311300 Zhejiang Province China
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28
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Tu T, Pang M, Jiang D, Zhou Y, Wu X, Yao X, Luo Y, Yang Z, Ren M, Lu A, Zhang G, Yu Y, Wang Y. Development of a Real-Time TaqMan RT-PCR Assay for the Detection of NADC34-like Porcine Reproductive and Respiratory Syndrome Virus. Vet Sci 2023; 10:vetsci10040279. [PMID: 37104434 PMCID: PMC10141196 DOI: 10.3390/vetsci10040279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/03/2023] [Accepted: 04/04/2023] [Indexed: 04/28/2023] Open
Abstract
NADC34-like porcine reproductive and respiratory syndrome virus first appeared in 2017 in a herd of pigs in Liaoning Province, China. The virus was subsequently found in other provinces. Given the potential for this virus to cause an epidemic, rapid, sensitive, and specific detection of NADC34-like PRRSV is required. The virus' ORF5 gene was artificially synthesized based on a Chinese reference strain, and specific primers/probes for the ORF5 gene were designed. Then, the amplified target fragment was cloned into the pMD19-T vector, and a series of diluted recombinant plasmids were used to generate a standard curve. An optimized real-time TaqMan RT-PCR method was established. The method was highly specific for NADC34-like PRRSV, without cross-reactions with other non-targeted pig viruses. The detection limit of this assay was 101 copies/μL. The method had an efficiency of 98.8%, a squared regression value (R2) of 0.999, and showed a linear range of 103-108 copies/μL of DNA per reaction. This method was shown to be analytically specific and sensitive with a low intra- and inter-assay coefficient of variation (<1.40%). A total of 321 clinical samples were tested using the established method, and four were shown to be positive (1.24%). This study confirmed the existence of NADC34-like PRRSV and HP-PRRSV co-infection in Sichuan and provided a promising alternative tool for the rapid detection of NADC34-like PRRSV.
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Affiliation(s)
- Teng Tu
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Maonan Pang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Dike Jiang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - You Zhou
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Xulong Wu
- Chengdu Agricultural College, Chengdu 611130, China
| | - Xueping Yao
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Yan Luo
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Zexiao Yang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
| | - Meishen Ren
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Aiping Lu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Ge Zhang
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yuanyuan Yu
- Law Sau Fai Institute for Advancing Translational Medicine in Bone and Joint Diseases (TMBJ), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-Based Translational Medicine and Drug Discovery (HKAP), Hong Kong SAR, China
- Institute of Integrated Bioinformedicine and Translational Science (IBTS), School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR, China
| | - Yin Wang
- Key Laboratory of Animal Diseases and Human Health of Sichuan Province, College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, China
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AboElkhair MA, Ahmed MM, Moustapha AEDH, Zaki AM, El Naggar RF, Elhamouly M, Anis A. Monitoring SARS-CoV-2 infection in different animal species and human in Egypt during 2020-2021. Biologia (Bratisl) 2023; 78:1-7. [PMID: 37363642 PMCID: PMC10021047 DOI: 10.1007/s11756-023-01362-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 02/17/2023] [Indexed: 03/28/2023]
Abstract
Coronaviruses cause respiratory and intestinal infections in animals and humans. By the end of 2019, there was an epidemic of novel coronavirus (COVID-19), which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Coronaviruses have a highly mutable genome that makes them genetically and phenotypically modifiable with a potential transmission to new host species. Based on current sequence databases, all human coronaviruses have animal origins, so animals have important roles in virus spillover to humans. The aim of this study is to investigate the role of different animal species in the epidemiology of SARS-CoV-2 in Egypt. A pan-coronaviruses RT-PCR has been used for detection of possible coronaviruses infection in different species including bats, humans, birds, and dogs in Egypt during the period of November 2020 till June 2021. Ninety-two samples (46 from Rousettus aegyptiacus bats, 10 from human, 26 from wild birds, and 10 from dogs) were screened for SARS-CoV-2. Our results revealed that only human samples were SARS-CoV-2 positive for SARS-CoV-2 while all other animal and bird samples were negative. To recapitulate, our results suggest that animals may not actively transmit SARS-CoV-2 among people in Egypt during the current COVID-19 pandemic. Further structural surveillance and follow up screening for SARS-CoV-2 among domestic and wild animal populations in Egypt is crucially needed.
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Affiliation(s)
- Mohammed A. AboElkhair
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
| | - Mohamed M. Ahmed
- Department of Biochemistry and Chemistry of Nutrition, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
| | - Alaa El Din H. Moustapha
- Department of Bacteriology, Mycology and Immunology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
| | - Ali Mohammed Zaki
- Department of Microbiology and Immunology, Faculty of Medicine, University of Ain-Shams, Cairo, 11591 Egypt
| | - Rania F. El Naggar
- Department of Virology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
| | - Moustafa Elhamouly
- Department of Histology and Cytology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
| | - Anis Anis
- Department of Pathology, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, 32897 Egypt
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30
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Oligonucleotide usage in coronavirus genomes mimics that in exon regions in host genomes. Virol J 2023; 20:39. [PMID: 36859385 PMCID: PMC9976658 DOI: 10.1186/s12985-023-01995-3] [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: 04/28/2022] [Accepted: 02/19/2023] [Indexed: 03/03/2023] Open
Abstract
BACKGROUND Viruses use various host factors for their growth, and efficient growth requires efficient use of these factors. Our previous study revealed that the occurrence frequency of oligonucleotides in the influenza virus genome is distinctly different among derived hosts, and the frequency tends to adapt to the host cells in which they grow. We aimed to study the adaptation mechanisms of a zoonotic virus to host cells. METHODS Herein, we compared the frequency of oligonucleotides in the genome of alpha- and betacoronavirus with those in the genomes of humans and bats, which are typical hosts of the viruses. RESULTS By comparing the oligonucleotide frequency in coronaviruses and their host genomes, we found a statistically tested positive correlation between the frequency of coronaviruses and that of the exon regions of the host from which the virus is derived. To examine the characteristics of early-stage changes in the viral genome, which are assumed to accompany the host change from non-humans to humans, we compared the oligonucleotide frequency between severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) at the beginning of the pandemic and the prevalent variants thereafter, and found changes towards the frequency of the host exon regions. CONCLUSIONS In alpha- and betacoronaviruses, the genome oligonucleotide frequency is thought to change in response to the cellular environment in which the virus is replicating, and actually the frequency has approached the frequency in exon regions in the host.
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31
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Chicken or Porcine Aminopeptidase N Mediates Cellular Entry of Pseudoviruses Carrying Spike Glycoprotein from the Avian Deltacoronaviruses HKU11, HKU13, and HKU17. J Virol 2023; 97:e0194722. [PMID: 36656013 PMCID: PMC9973037 DOI: 10.1128/jvi.01947-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Members of deltacoronavirus (DCoV) have mostly been identified in diverse avian species as natural reservoirs, though the porcine DCoV (PDCoV) is a major swine enteropathogenic virus with global spread. The important role of aminopeptidase N (APN) orthologues from various mammalian and avian species in PDCoV cellular entry and interspecies transmission has been revealed recently. In this study, comparative analysis indicated that three avian DCoVs, bulbul DCoV HKU11, munia DCoV HKU13, and sparrow DCoV HKU17 (Chinese strain), and PDCoV in the subgenera Buldecovirus are grouped together at whole-genome levels; however, the spike (S) glycoprotein and its S1 subunit of HKU17 are more closely related to night heron DCoV HKU19 in Herdecovirus. Nevertheless, the S1 protein of HKU11, HKU13, or HKU17 bound to or interacted with chicken APN (chAPN) or porcine APN (pAPN) by flow cytometry analysis of cell surface expression of APN and by coimmunoprecipitation in APN-overexpressing cells. Expression of chAPN or pAPN allowed entry of pseudotyped lentiviruses with the S proteins from HKU11, HKU13 and HKU17 into nonsusceptible cells and natural avian and porcine cells, which could be inhibited by the antibody against APN or anti-PDCoV-S1. APN knockdown by siRNA or knockout by CRISPR/Cas9 in chicken or swine cell lines significantly or almost completely blocked infection of these pseudoviruses. Hence, we demonstrate that HKU11, HKU13, and HKU17 with divergent S genes likely engage chAPN or pAPN to enter the cells, suggesting a potential interspecies transmission from wild birds to poultry and from birds to mammals by certain avian DCoVs. IMPORTANCE The receptor usage of avian deltacoronaviruses (DCoVs) has not been investigated thus far, though porcine deltacoronavirus (PDCoV) has been shown to utilize aminopeptidase N (APN) as a cell receptor. We report here that chicken or porcine APN also mediates cellular entry by three avian DCoV (HKU11, HKU13, and HKU17) spike pseudoviruses, and the S1 subunit of three avian DCoVs binds to APN in vitro and in the surface of avian and porcine cells. The results fill the gaps in knowledge about the avian DCoV receptor and elucidate important insights for the monitoring and prevention of potential interspecies transmission of certain avian DCoVs. In view of the diversity of DCoVs, whether this coronavirus genus will cause novel virus to emerge in other mammals from birds, are worthy of further surveillance and investigation.
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [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: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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Abstract
Zoonoses are diseases and infections naturally transmitted between humans and vertebrate animals. Over the years, zoonoses have become increasingly significant threats to global health. They form the dominant group of diseases among the emerging infectious diseases (EID) and currently account for 73% of EID. Approximately 25% of zoonoses originate in domestic animals. The etiological agents of zoonoses include different pathogens, with viruses accounting for approximately 30% of all zoonotic infections. Zoonotic diseases can be transmitted directly or indirectly, by contact, via aerosols, through a vector, or vertically in utero. Zoonotic diseases are found in every continent except Antarctica. Numerous factors associated with the pathogen, human activities, and the environment play significant roles in the transmission and emergence of zoonotic diseases. Effective response and control of zoonotic diseases call for multiple-sector involvement and collaboration according to the One Health concept.
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Affiliation(s)
- Oyewale Tomori
- African Centre of Excellence for Genomics of Infectious Diseases (ACEGID), Redeemer's University, Ede, Nigeria; ,
| | - Daniel O Oluwayelu
- Department of Veterinary Microbiology and Centre for Control and Prevention of Zoonoses, University of Ibadan, Ibadan, Oyo State, Nigeria; ,
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Yousef A, Bozkurt F, Abdeljawad T, Emreizeeq E. A mathematical model of COVID-19 and the multi fears of the community during the epidemiological stage. JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS 2023; 419:114624. [PMID: 35966169 PMCID: PMC9361582 DOI: 10.1016/j.cam.2022.114624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/01/2022] [Indexed: 06/15/2023]
Abstract
Within two years, the world has experienced a pandemic phenomenon that changed almost everything in the macro and micro-environment; the economy, the community's social life, education, and many other fields. Governments started to collaborate with health institutions and the WHO to control the pandemic spread, followed by many regulations such as wearing masks, maintaining social distance, and home office work. While the virus has a high transmission rate and shows many mutated forms, another discussion appeared in the community: the fear of getting infected and the side effects of the produced vaccines. The community started to face uncertain information spread through some networks keeping the discussions of side effects on-trend. However, this pollution spread confused the community more and activated multi fears related to the virus and the vaccines. This paper establishes a mathematical model of COVID-19, including the community's fear of getting infected and the possible side effects of the vaccines. These fears appeared from uncertain information spread through some social sources. Our primary target is to show the psychological effect on the community during the pandemic stage. The theoretical study contains the existence and uniqueness of the IVP and, after that, the local stability analysis of both equilibrium points, the disease-free and the positive equilibrium point. Finally, we show the global asymptotic stability holds under specific conditions using a suitable Lyapunov function. In the end, we conclude our theoretical findings with some simulations.
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Affiliation(s)
- Ali Yousef
- Kuwait College of Science and Technology, Department of Mathematics, 27235 Kuwait City, Kuwait
| | - Fatma Bozkurt
- Kuwait College of Science and Technology, Department of Mathematics, 27235 Kuwait City, Kuwait
- Erciyes University, Department of Mathematics, 38039 Kayseri, Turkiye
| | - Thabet Abdeljawad
- Prince Sultan University, Department of Mathematics and Sciences, 11586 Riyadh, Saudi Arabia
- China Medical University, Department of Medical Research, 40402 Taichung, Taiwan
| | - Emad Emreizeeq
- Abu Dhabi Polytechnic, Department of Mathematics, 111499 Abu Dhabi, United Arab Emirates
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de Araujo IG, Pattaro-Júnior JR, Barbosa CG, Philippsen GS, Silva AR, Ioshino RS, Moraes CB, Freitas-Junior LH, Barros L, Peralta RM, Fernandez MA, Seixas FAV. Potential of plant extracts in targeting SARS-CoV-2 main protease: an in vitro and in silico study. J Biomol Struct Dyn 2023; 41:12204-12213. [PMID: 36651196 DOI: 10.1080/07391102.2023.2166589] [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: 08/29/2022] [Accepted: 01/01/2023] [Indexed: 01/19/2023]
Abstract
The deaths caused by the covid-19 pandemic have recently decreased due to a worldwide effort in vaccination campaigns. However, even vaccinated people can develop a severe form of the disease that requires ICU admission. As a result, the search for antiviral drugs to treat these severe cases has become a necessity. In this context, natural products are an interesting alternative to synthetic medicines used in drug repositioning, as they have been consumed for a long time through traditional medicine. Many natural compounds found in plant extracts have already been shown to be effective in treating viral and bacterial diseases, making them possible hits to exploit against covid-19. The objective of this work was to evaluate the antiviral activity of different plant extracts available in the library of natural products of the Universidade Estadual de Maringá, by inhibiting the SARS-CoV-2 main protease (Mpro), and by preventing viral infection in a cellular model. As a result, the extract of Cytinus hypocistis, obtained by ultrasound, showed a Mpro inhibition capacity greater than 90%. In the infection model assays using Vero cells, an inhibition of 99.6% was observed, with a selectivity index of 42.7. The in silico molecular docking simulations using the extract compounds against Mpro, suggested Tellimagrandin II as the component of C. hypocistis extract most likely to inhibit the viral enzyme. These results demonstrate the potential of C. hypocistis extract as a promising source of natural compounds with antiviral activity against covid-19.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Cecilia Gomes Barbosa
- Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
- Universidade Municipal de São Caetano do Sul (USCS), São Caetano, Brazil
- Bela Vista, São Paulo, Brazil
| | | | - Ana Rita Silva
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha, (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
- Departamento de Ciencias Farmacéuticas, Facultad de Farmacia, CIETUS-IBSAL, Universidad de Salamanca, Salamanca, España
| | | | | | | | - Lillian Barros
- Centro de Investigação de Montanha (CIMO), Instituto Politécnico de Bragança, Bragança, Portugal
- Laboratório Associado para a Sustentabilidade e Tecnologia em Regiões de Montanha, (SusTEC), Instituto Politécnico de Bragança, Bragança, Portugal
| | | | - Maria Aparecida Fernandez
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Maringá, P.R. Brazil
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Kia V, Eshaghi-Gorji R, Mansour RN, Hassannia H, Hasanzadeh E, Gheibi M, Mellati A, Enderami SE. Mesenchymal Stromal Cells and their EVs as Potential Leads for SARSCoV2 Treatment. Curr Stem Cell Res Ther 2023; 18:35-53. [PMID: 35473518 DOI: 10.2174/1574888x17666220426115831] [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: 07/30/2021] [Revised: 12/17/2021] [Accepted: 01/28/2022] [Indexed: 11/22/2022]
Abstract
In December 2019, a betacoronavirus was isolated from pneumonia cases in China and rapidly turned into a pandemic of COVID-19. The virus is an enveloped positive-sense ssRNA and causes a severe respiratory syndrome along with a cytokine storm, which is the main cause of most complications. Therefore, treatments that can effectively control the inflammatory reactions are necessary. Mesenchymal Stromal Cells and their EVs are well-known for their immunomodulatory effects, inflammation reduction, and regenerative potentials. These effects are exerted through paracrine secretion of various factors. Their EVs also transport various molecules such as microRNAs to other cells and affect recipient cells' behavior. Scores of research and clinical trials have indicated the therapeutic potential of EVs in various diseases. EVs also seem to be a promising approach for severe COVID-19 treatment. EVs have also been used to develop vaccines since EVs are biocompatible nanoparticles that can be easily isolated and engineered. In this review, we have focused on the use of Mesenchymal Stromal Cells and their EVs for the treatment of COVID-19, their therapeutic capabilities, and vaccine development.
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Affiliation(s)
- Vahid Kia
- Department of Medical Biotechnology, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Reza Eshaghi-Gorji
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | | | - Hadi Hassannia
- Immunogenetics Research Center, School of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Amol Faculty of Paramedical Sciences, Mazandaran University of Medical Sciences, Sari, Iran
| | - Elham Hasanzadeh
- Department of Tissue Engineering and Regenerative Medicine, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mobina Gheibi
- Student Research Committee, Mazandaran University of Medical Sciences, Sari, Iran
| | - Amir Mellati
- Department of Tissue Engineering and Regenerative Medicine, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Seyed Ehsan Enderami
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran.,Department of Medical Biotechnology, Faculty of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
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Khushboo, Siddiqi NJ, Sharma B. Pathophysiology of SARS-CoV2 Mediated Depression, Therapeutics, and Consequences: A Comprehensive Narrative. Mini Rev Med Chem 2023; 23:217-229. [PMID: 35658879 DOI: 10.2174/1381612828666220603150637] [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: 02/08/2022] [Revised: 03/31/2022] [Accepted: 04/13/2022] [Indexed: 11/22/2022]
Abstract
The Coronavirus Disease 2019 (COVID-19), caused by Severe Acute Respiratory Syndrome Coronavirus type 2 (SARS-CoV-2), belongs to emerging and reemerging diseases, which was first identified and reported in Wuhan, China, in December 2019. The genetic sequence of SARS-CoV-2 was similar to the SARS virus, a β-coronavirus. The epidemiological studies suggest that the transmission of SARS-CoV-2 mainly occurs from an infected person to others through close contact with the respiratory droplets or by having contact with SARS-CoV-2 adhering to objects and surfaces. The incubation period ranges from 5 to14 days. The symptoms include fever, dry cough, tiredness, aches, chest pain, conjunctivitis, diarrhea, headache, difficulty in breathing or short breath, loss of taste, smell, rashes on the skin, and sore throat. Some reports indicated that males exhibited lower scores than females, the younger populations displayed increased symptoms, Chinese/Taiwanese people registered only scarce symptoms, and Canadians experienced more symptoms. The results of several studies suggested that while COVID-19 had a significant effect on depression, job instability affected anxiety and depression. The diagnostics to detect the presence of coronavirus involve ELISA and RT-PCR. There is no specific treatment available to eradicate COVID-19. The therapeutics used to treat COVID 19 exhibited severe side effects. Recently, some Indian traditional medicinal plants have shown promise in reducing the risk of viral infection and also boosting the immunity of an individual. This paper presents an overview of the current status of depression in the SARS CoV2 infected people and the measures required to overcome COVID-19 induced depression in patients even after recovery.
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Affiliation(s)
- Khushboo
- Departments of Biochemistry, University of Allahabad, Allahabad 211002, UP-India
| | - Nikhat J Siddiqi
- Department of Biochemistry, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Bechan Sharma
- Departments of Biochemistry, University of Allahabad, Allahabad 211002, UP-India
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38
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Identification of a novel linear B-cell epitope in porcine deltacoronavirus nucleocapsid protein. Appl Microbiol Biotechnol 2023; 107:651-661. [PMID: 36602561 PMCID: PMC9813470 DOI: 10.1007/s00253-022-12348-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 11/29/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023]
Abstract
Porcine deltacoronavirus (PDCoV) is an emerging swine enteropathogenic coronavirus that caused diarrhea and/or vomiting in neonatal piglets worldwide. Coronaviruses nucleocapsid (N) protein is the most conserved structural protein for viral replication and possesses good antigenicity. In this study, three monoclonal antibodies (mAbs), 3B4, 4D3, and 4E3 identified as subclass IgG2aκ were prepared using the lymphocytic hybridoma technology against PDCoV N protein. Furthermore, the B-cell epitope recognized by mAb 4D3 was mapped by dozens of overlapping truncated recombinant proteins based on the western blotting. The polypeptide 28QFRGNGVPLNSAIKPVE44 (EP-4D3) in the N-terminal of PDCoV N protein was identified as the minimal linear epitope for binding mAb 4D3. And the EP-4D3 epitope's amino acid sequence homology study revealed that PDCoV strains are substantially conserved, with the exception of the Alanine43 substitution Valine43 in the China lineage, the Early China lineage, and the Thailand, Vietnam, and Laos lineage. The epitope sequences shared high similarity (94.1%) with porcine coronavirus HKU15-155 (PorCoV HKU15), Asian leopard cats coronavirus (ALCCoV), sparrow coronavirus HKU17 (SpCoV HKU17), and sparrow deltacoronavirus. In contrast, the epitope sequences shared a very low homology (11.8 to 29.4%) with other porcine CoVs (PEDV, TGEV, PRCV, SADS-CoV, PHEV). Overall, the study will enrich the biological function of PDCoV N protein and provide foundational data for further development of diagnostic applications. KEY POINTS: • Three monoclonal antibodies against PDCoV N protein were prepared. • Discovery of a novel B-cell liner epitope (28QFRGNGVPLNSAIKPVE44) of PDCoV N protein. • The epitope EP-4D3 was conserved among PDCoV strains.
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Moraga-Fernández A, Sánchez-Sánchez M, Queirós J, Lopes AM, Vicente J, Pardavila X, Sereno-Cadierno J, Alves PC, de la Fuente J, Fernández de Mera IG. A study of viral pathogens in bat species in the Iberian Peninsula: identification of new coronavirus genetic variants. Int J Vet Sci Med 2022; 10:100-110. [PMID: 36407496 PMCID: PMC9639555 DOI: 10.1080/23144599.2022.2139985] [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] [Indexed: 11/06/2022] Open
Abstract
Bats have long been associated with multiple pathogens, including viruses affecting humans such as henipaviruses, filoviruses, bunyaviruses and coronaviruses. The alpha and beta coronaviruses genera can infect most mammalian species. Among them, betacoronavirus SARS-CoV, MERS-CoV and SARS-CoV-2, which have caused the three major pandemics in the last two decades, have been proposed to originate in bats. In this study, 194 oral swabs from 22 bats species sampled in 19 locations of the Iberian Peninsula were analysed and characterized by three different PCR tests (coronavirus generic real-time RT-PCR, multiplex conventional PCR, and SARS-CoV-2 specific real-time RT-PCR) to detect bat coronaviruses. Screening with coronavirus generic PCR showed 102 positives out of 194 oral swabs analysed. Then, metabarcoding with multiplex PCR amplified 15 positive samples. Most of the coronaviruses detected in this study belong to alphacoronavirus (α-CoV) genus, with multiple alphacoronaviruses identified by up to five different genetic variants coexisting in the same bat. One of the positive samples identified in a Miniopterus schreibersii bat positive for the generic coronavirus PCR and the specific SARS-CoV-2 PCR was classified as betacoronavirus (-CoV) through phylogenetic analysis. These results support the rapid evolution of coronaviruses to generate new genomic potentially pathogenic variants likely through co-infection and recombination.
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Affiliation(s)
- Alberto Moraga-Fernández
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Marta Sánchez-Sánchez
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - João Queirós
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Estação Biológica de Mértola (EBM), CIBIO, Praça Luís de Camões, Mértola, Portugal
| | - Ana M. Lopes
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
| | - Joaquín Vicente
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Xosé Pardavila
- Sorex, Ecoloxía e Medio Ambiente S.L., Santiago de Compostela. A Coruña, Spain
| | - Jorge Sereno-Cadierno
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
| | - Paulo C. Alves
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Estação Biológica de Mértola (EBM), CIBIO, Praça Luís de Camões, Mértola, Portugal
- Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - José de la Fuente
- Institute for Game and Wildlife Research, IREC (CSIC-UCLM-JCCM), SaBio Research Group, Ciudad Real, Spain
- Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, USA
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Santos FRDS, de Azevedo MSP, Bielavsky M, da Costa HHM, Ribeiro DG, Nascimento GGD, Marcondes GMP, de Castro BP, de Lima Neto DF, Prudencio CR. Mutational profile confers increased stability of SARS-CoV-2 spike protein in Brazilian isolates. J Biomol Struct Dyn 2022; 40:13184-13189. [PMID: 34633892 DOI: 10.1080/07391102.2021.1982775] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Spike (S) protein has been recognized as a promising molecular target for diagnostic, vaccines and antiviral drugs development for COVID-19. In this study, we analyzed the most predominant mutations in the S protein of Brazilian isolates and predicted the effect of these amino acid alterations to protein conformation. A total of 25,924 sequences were obtained from GISAID for five regions of Brazilian territory (Midwest, North, Northeast, South, and Southeast), according to exclusion criteria. Most of the SARS-CoV-2 isolates belongs to the G clade and showed a large occurrence of D614G, N501Y and L18F substitutions. Prediction effects of these amino acid substitutions on the structure dynamics of the spike protein indicated a positive ΔΔG values and negative ΔΔSVib in most cases which is associated to structural stabilization and flexibility reduction of the S protein. Mutations E484K, N501Y and K417N belong to several SARS-CoV-2 variants of concern such as Alpha, Beta, Gamma and Delta, and showed high incidence among Brazilian isolates. These mutations have been described to increase RBD affinity to ACE-2 host and abolishment of RBD affinity to potent neutralizing ant-RBD. The increase in rates of infection and reinfection requires continuous genomic surveillance studies in order to characterize emerging mutations and monitor vaccine efficacy, and thus consideration structural data and dynamics in the observed phenotypes.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | - Monica Bielavsky
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | - Daniela Gomes Ribeiro
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
| | | | | | | | - Daniel Ferreira de Lima Neto
- Coordenação-Geral de Laboratórios de Saúde Pública, Secretaria de Vigilância em Saúde, Ministério da Saúde, Brasília, Distrito Federal, Brazil.,Laboratório de Termodinâmica de Proteínas, Departamento de Bioquímica, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | - Carlos Roberto Prudencio
- Laboratory of Immunotechnology, Center of Immunology, Adolfo Lutz Institute, São Paulo, SP, Brazil
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Faye MN, Barry MA, Jallow MM, Wade SF, Mendy MP, Sy S, Fall A, Kiori DE, Ndiaye NK, Goudiaby D, Diamanka A, Niang MN, Dia N. Epidemiology of Non-SARS-CoV2 Human Coronaviruses (HCoVs) in People Presenting with Influenza-like Illness (ILI) or Severe Acute Respiratory Infections (SARI) in Senegal from 2012 to 2020. Viruses 2022; 15:20. [PMID: 36680061 PMCID: PMC9864203 DOI: 10.3390/v15010020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/14/2022] [Indexed: 12/24/2022] Open
Abstract
In addition to emerging coronaviruses (SARS-CoV, MERS, SARS-CoV-2), there are seasonal human coronaviruses (HCoVs): HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1. With a wide distribution around the world, HCoVs are usually associated with mild respiratory disease. In the elderly, young children and immunocompromised patients, more severe or even fatal respiratory infections may be observed. In Africa, data on seasonal HCoV are scarce. This retrospective study investigated the epidemiology and genetic diversity of seasonal HCoVs during nine consecutive years of influenza-like illness surveillance in Senegal. Nasopharyngeal swabs were collected from ILI outpatients or from SARI hospitalized patients. HCoVs were diagnosed by qRT-PCR and the positive samples were selected for molecular characterization. Among 9337 samples tested for HCoV, 406 (4.3%) were positive: 235 (57.9%) OC43, 102 (25.1%) NL63, 58 (14.3%) 229E and 17 (4.2%) HKU1. The four types circulated during the study period and a peak was noted between November and January. Children under five were the most affected. Co-infections were observed between HCoV types (1.2%) or with other viruses (76.1%). Genetically, HCoVs types showed diversity. The results highlighted that the impact of HCoVs must be taken into account in public health; monitoring them is therefore particularly necessary both in the most sensitive populations and in animals.
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Affiliation(s)
- Modeste Name Faye
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Mamadou Aliou Barry
- Epidemiology, Clinical Research and Data Science Department, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Mamadou Malado Jallow
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Serigne Fallou Wade
- Ecole Supérieure des Sciences Agricoles et de l’Alimentation (ES2A), Université Amadou Makhtar MBOW de Dakar (UAM), Dakar 12900, Senegal
| | - Marie Pedapa Mendy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | - Sara Sy
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Amary Fall
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Davy Evrard Kiori
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | | | - Deborah Goudiaby
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
| | - Arfang Diamanka
- Département de Biologie Animale, Faculté des Sciences et Techniques, Université Cheikh Anta DIOP de Dakar, Dakar 12900, Senegal
| | | | - Ndongo Dia
- Département de Virologie, Institut Pasteur de Dakar, Dakar 12900, Senegal
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Šimičić P, Židovec-Lepej S. A Glimpse on the Evolution of RNA Viruses: Implications and Lessons from SARS-CoV-2. Viruses 2022; 15:1. [PMID: 36680042 PMCID: PMC9866536 DOI: 10.3390/v15010001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
RNA viruses are characterised by extremely high genetic variability due to fast replication, large population size, low fidelity, and (usually) a lack of proofreading mechanisms of RNA polymerases leading to high mutation rates. Furthermore, viral recombination and reassortment may act as a significant evolutionary force among viruses contributing to greater genetic diversity than obtainable by mutation alone. The above-mentioned properties allow for the rapid evolution of RNA viruses, which may result in difficulties in viral eradication, changes in virulence and pathogenicity, and lead to events such as cross-species transmissions, which are matters of great interest in the light of current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemics. In this review, we aim to explore the molecular mechanisms of the variability of viral RNA genomes, emphasising the evolutionary trajectory of SARS-CoV-2 and its variants. Furthermore, the causes and consequences of coronavirus variation are explored, along with theories on the origin of human coronaviruses and features of emergent RNA viruses in general. Finally, we summarise the current knowledge on the circulating variants of concern and highlight the many unknowns regarding SARS-CoV-2 pathogenesis.
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Affiliation(s)
| | - Snježana Židovec-Lepej
- Department of Immunological and Molecular Diagnostics, University Hospital for Infectious Diseases “Dr. Fran Mihaljević”, HR-10000 Zagreb, Croatia
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43
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Dylus D, Altenhoff A, Majidian S, Sedlazeck FJ, Dessimoz C. Read2Tree: scalable and accurate phylogenetic trees from raw reads. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.04.18.488678. [PMID: 36561179 PMCID: PMC9774205 DOI: 10.1101/2022.04.18.488678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The inference of phylogenetic trees is foundational to biology. However, state-of-the-art phylogenomics requires running complex pipelines, at significant computational and labour costs, with additional constraints in sequencing coverage, assembly and annotation quality. To overcome these challenges, we present Read2Tree, which directly processes raw sequencing reads into groups of corresponding genes. In a benchmark encompassing a broad variety of datasets, our assembly-free approach was 10-100x faster than conventional approaches, and in most cases more accurate-the exception being when sequencing coverage was high and reference species very distant. To illustrate the broad applicability of the tool, we reconstructed a yeast tree of life of 435 species spanning 590 million years of evolution. Applied to Coronaviridae samples, Read2Tree accurately classified highly diverse animal samples and near-identical SARS-CoV-2 sequences on a single tree-thereby exhibiting remarkable breadth and depth. The speed, accuracy, and versatility of Read2Tree enables comparative genomics at scale.
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Affiliation(s)
- David Dylus
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- present address: F. Hoffmann-La Roche Ltd, Immunology, Infectious Disease, and Ophthalmology (I2O), Roche Pharmaceutical Research and Early Development (pRED), Basel, 4070, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Adrian Altenhoff
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, ETH, 8092 Zurich, Switzerland
| | - Sina Majidian
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, 77030, USA
- Department of Computer Science, Rice University, Houston, TX, 77005, USA
| | - Christophe Dessimoz
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
- SIB Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Department of Computer Science, University College London, London WC1E 6BT, UK
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E, UK
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44
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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.
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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
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Silva CS, Tryndyak VP, Camacho L, Orloff MS, Porter A, Garner K, Mullis L, Azevedo M. Temporal dynamics of SARS-CoV-2 genome and detection of variants of concern in wastewater influent from two metropolitan areas in Arkansas. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 849:157546. [PMID: 35914602 PMCID: PMC9338166 DOI: 10.1016/j.scitotenv.2022.157546] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/14/2022] [Accepted: 07/17/2022] [Indexed: 06/15/2023]
Abstract
Although SARS-CoV-2 can cause severe illness and death, a percentage of the infected population is asymptomatic. This, along with other factors, such as insufficient diagnostic testing and underreporting due to self-testing, contributes to the silent transmission of SARS-CoV-2 and highlights the importance of implementing additional surveillance tools. The fecal shedding of the virus from infected individuals enables its detection in community wastewater, and this has become a valuable public health tool worldwide as it allows the monitoring of the disease on a populational scale. Here, we monitored the presence of SARS-CoV-2 and its dynamic genomic changes in wastewater sampled from two metropolitan areas in Arkansas during major surges of COVID-19 cases and assessed how the viral titers in these samples related to the clinical case counts between late April 2020 and January 2022. The levels of SARS-CoV-2 RNA were quantified by reverse-transcription quantitative polymerase chain reaction (RT-qPCR) using a set of TaqMan assays targeting three different viral genes (encoding ORF1ab polyprotein, surface glycoprotein, and nucleocapsid phosphoprotein). An allele-specific RT-qPCR approach was used to screen the samples for SARS-CoV-2 mutations. The identity and genetic diversity of the virus were further investigated through amplicon-based RNA sequencing, and SARS-CoV-2 variants of concern were detected in wastewater samples throughout the duration of this study. Our data show how changes in the virus genome can affect the sensitivity of specific RT-qPCR assays used in COVID-19 testing with the surge of new variants. A significant association was observed between viral titers in wastewater and recorded number of COVID-19 cases in the areas studied, except when assays failed to detect targets due to the presence of particular variants. These findings support the use of wastewater surveillance as a reliable complementary tool for monitoring SARS-CoV-2 and its genetic variants at the community level.
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Affiliation(s)
- Camila S Silva
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
| | - Volodymyr P Tryndyak
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Luísa Camacho
- Division of Biochemical Toxicology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Mohammed S Orloff
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Center for the Studies of Tobacco, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Austin Porter
- Department of Health Policy and Management, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Kelley Garner
- Department of Epidemiology, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR, USA; Arkansas Department of Health, Little Rock, AR, USA
| | - Lisa Mullis
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
| | - Marli Azevedo
- Division of Microbiology, National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA
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Kopel J, Fralick J, Reid TW. The Potential Antiviral Effects of Selenium Nanoparticles and Coated Surfaces. Antibiotics (Basel) 2022; 11:antibiotics11121683. [PMID: 36551339 PMCID: PMC9774352 DOI: 10.3390/antibiotics11121683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 11/24/2022] Open
Abstract
Modern epidemics quickly spread across borders and continents with devastating effects on both human health and the world economy. This issue is made worse by the various ways that infections are spread, including through aerosol, droplets, and fomites. The antibacterial qualities of various surface materials and coatings have been the subject of much research. However, the antiviral activity of metal coatings can be heavily influenced by imbalances in metal distribution and the presence of other metal impurities. As such, there is interest in developing novel surface coatings that can reduce the transmission of active viral particles in healthcare facilities. In recent years, the non-metals, such as selenium and nanoparticles, have acquired greater interest from the medical and scientific community for their antiviral surface activity. In this review, we will discuss the cellular and physiological functions of selenium in mammalian cells and against viral infections. We then discuss the mechanism behind selenium coated surfaces and their efficacy against bacterial infections. Lastly, we examine the antiviral activity of selenium, and the potential antiviral activity of selenium nanoparticles and coatings.
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Affiliation(s)
- Jonathan Kopel
- School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence:
| | - Joe Fralick
- Department of Immunology and Molecular Microbiology, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Ted W. Reid
- Department of Ophthalmology and Visual Sciences, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
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Mahroum N, Seida I, Esirgün SN, Bragazzi NL. The COVID-19 pandemic - How many times were we warned before? Eur J Intern Med 2022; 105:8-14. [PMID: 35864073 PMCID: PMC9289047 DOI: 10.1016/j.ejim.2022.07.009] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/01/2022] [Accepted: 07/05/2022] [Indexed: 11/04/2022]
Abstract
Infectious diseases are known to act in both predictable and unpredictable ways, which leads to the notions of emerging and reemerging infectious diseases. Emerging diseases with their disastrous consequences might be surprising and unpredictable, but they could be foreseen. For instance, some emerging diseases and recently the coronavirus disease 2019 (COVID-19) were the reason for papers published by the World Health Organization (WHO) and other researchers addressing the likely pathogens causing future outbreaks, according to the reports of the WHO in 2016 and 2018. Although it might seem like a wisdom in retrospect, several studies had already indicated possible future outbreaks caused by coronaviruses. Announcements, which may be viewed as "warnings," appeared since the emergence of the first coronavirus-related outbreak caused by severe acute respiratory syndrome coronavirus (SARS-CoV) in the winter of 2002-2003 and a later outbreak caused by the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012-2013. Therefore, we were curious to review the medical literature prior to the COVID-19 pandemic with an aim to enumerate and evaluate studies addressing and warning against future outbreaks, and surprisingly pandemics, of members of coronaviruses. Interestingly, we found numerous studies that correctly predicted the current pandemic of COVID-19. While this part is highly interesting, how authorities reacted and prepared for warnings, if any, and how will they get prepared for the next warnings are our main messages. Taking these points into serious consideration will certainly aid in analyzing reports regarding possible future outbreaks as well as in developing various strategies for prevention and coping with such epidemics.
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Affiliation(s)
- Naim Mahroum
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey.
| | - Isa Seida
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey
| | - Sevval Nil Esirgün
- International School of Medicine, Istanbul Medipol University, Göztepe Mah, Atatürk Cd. No:40, Beykoz, Istanbul 34810, Turkey
| | - Nicola Luigi Bragazzi
- Laboratory for Industrial and Applied Mathematics (LIAM), Department of Mathematics and Statistics, York University, Toronto, Canada
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Ch’ng L, Tsang SM, Ong ZA, Low DH, Wiantoro S, Smith IL, Simmons NB, Su YC, Lohman DJ, Smith GJ, Mendenhall IH. Co-circulation of alpha- and beta-coronaviruses in Pteropus vampyrus flying foxes from Indonesia. Transbound Emerg Dis 2022; 69:3917-3925. [PMID: 36382687 PMCID: PMC9898127 DOI: 10.1111/tbed.14762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 10/03/2022] [Accepted: 11/11/2022] [Indexed: 11/17/2022]
Abstract
Bats are important reservoirs for alpha- and beta-coronaviruses. Coronaviruses (CoV) have been detected in pteropodid bats from several Southeast Asian countries, but little is known about coronaviruses in the Indonesian archipelago in proportion to its mammalian biodiversity. In this study, we screened pooled faecal samples from the Indonesian colonies of Pteropus vampyrus with unbiased next-generation sequencing. Bat CoVs related to Rousettus leschenaultii CoV HKU9 and Eidolon helvum CoV were detected. The 121 faecal samples were further screened using a conventional hemi-nested pan-coronavirus PCR assay. Three positive samples were successfully sequenced, and phylogenetic reconstruction revealed the presence of alpha- and beta-coronaviruses. CoVs belonging to the subgenera Nobecovirus, Decacovirus and Pedacovirus were detected in a single P. vampyrus roost. This study expands current knowledge of coronavirus diversity in Indonesian flying foxes, highlighting the need for longitudinal surveillance of colonies as continuing urbanization and deforestation heighten the risk of spillover events.
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Affiliation(s)
- Lena Ch’ng
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Susan M. Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines
| | - Zoe A. Ong
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Dolyce H.W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Sigit Wiantoro
- Museum Zoologicum Bogoriense, Research Center for Biosystematics and Evolution, National Research and Innovation Agency, Cibinong, West Java 16911, Indonesia
| | - Ina L. Smith
- Health and Biosecurity, The Commonwealth Scientific and Industrial Research Organization, Black Mountain, ACT 2601, Australia
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Yvonne C.F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - David J. Lohman
- Biology Department, City College of New York, City University of New York, New York, NY 10031, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY 10016, USA
- Zoology Division, National Museum of Natural History, Manila 1000, Philippines
| | - Gavin J.D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- Centre for Outbreak Preparedness, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore
- Duke Global Health Institute, Duke University, Durham, NC 27710, USA
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore 168753, Singapore
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Mannsverk S, Bergholm J, Palanisamy N, Ellström P, Kaden R, Lindh J, Lennerstrand J. SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. Virol J 2022; 19:164. [PMID: 36258215 DOI: 10.1186/s12985-022-01896-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. METHODS We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. RESULTS The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. CONCLUSION Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences.
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Affiliation(s)
- Steinar Mannsverk
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, 752 37, Uppsala, Sweden
| | - Julia Bergholm
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - René Kaden
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lindh
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.
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50
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Quinteros JA, Noormohammadi AH, Lee SW, Browning GF, Diaz‐Méndez A. Genomics and pathogenesis of the avian coronavirus infectious bronchitis virus. Aust Vet J 2022; 100:496-512. [PMID: 35978541 PMCID: PMC9804484 DOI: 10.1111/avj.13197] [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: 04/13/2022] [Revised: 04/25/2022] [Accepted: 05/02/2022] [Indexed: 01/05/2023]
Abstract
Infectious bronchitis virus (IBV) is a member of the family Coronaviridae, together with viruses such as SARS-CoV, MERS-CoV and SARS-CoV-2 (the causative agent of the COVID-19 global pandemic). In this family of viruses, interspecies transmission has been reported, so understanding their pathobiology could lead to a better understanding of the emergence of new serotypes. IBV possesses a single-stranded, non-segmented RNA genome about 27.6 kb in length that encodes several non-structural and structural proteins. Most functions of these proteins have been confirmed in IBV, but some other proposed functions have been based on research conducted on other members of the family Coronaviridae. IBV has variable tissue tropism depending on the strain, and can affect the respiratory, reproductive, or urinary tracts; however, IBV can also replicate in other organs. Additionally, the pathogenicity of IBV is also variable, with some strains causing only mild clinical signs, while infection with others results in high mortality rates in chickens. This paper extensively and comprehensibly reviews general aspects of coronaviruses and, more specifically, IBV, with emphasis on protein functions and pathogenesis. The pathogenicity of the Australian strains of IBV is also reviewed, describing the variability between the different groups of strains, from the classical to the novel and recombinant strains. Reverse genetic systems, cloning and cell culture growth techniques applicable to IBV are also reviewed.
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Affiliation(s)
- JA Quinteros
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia,Present address:
Escuela de Ciencias Agrícolas y VeterinariasUniversidad Viña del Mar, Agua Santa 7055 2572007Viña del MarChile
| | - AH Noormohammadi
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneWerribeeVictoriaAustralia
| | - SW Lee
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia,College of Veterinary MedicineKonkuk UniversitySeoulRepublic of Korea
| | - GF Browning
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
| | - A Diaz‐Méndez
- Asia‐Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVictoriaAustralia
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