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Hoferle PJ, Anderson TK, Kirchdoerfer RN. A genus-specific nsp12 region impacts polymerase assembly in Alpha- and Gammacoronaviruses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.23.604833. [PMID: 39091740 PMCID: PMC11291119 DOI: 10.1101/2024.07.23.604833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Coronavirus relevancy for human health has surged over the past 20 years as they have a propensity for spillover into humans from animal reservoirs resulting in pandemics such as COVID-19. The diversity within the Coronavirinae subfamily and high infection frequency in animal species worldwide creates a looming threat that calls for research across all genera within the Coronavirinae subfamily. We sought to contribute to the limited structural knowledge within the Gammacoronavirus genera and determined the structure of the viral core replication-transcription complex (RTC) from Infectious Bronchitis Virus (IBV) using single-particle cryo-EM. Comparison between our IBV structure with published RTC structures from other Coronavirinae genera reveals structural differences across genera. Using in vitro biochemical assays, we characterized these differences and revealed their differing involvement in core RTC formation across different genera. Our findings highlight the value of cross-genera Coronavirinae studies, as they show genera specific features in coronavirus genome replication. A broader knowledge of coronavirus replication will better prepare us for future coronavirus spillovers.
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Affiliation(s)
- Peter J. Hoferle
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Thomas K. Anderson
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Robert N. Kirchdoerfer
- Department of Biochemistry, Institute for Molecular Virology, Center for Quantitative Cell Imaging, University of Wisconsin-Madison, Madison, Wisconsin 53706
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2
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Tian Y, Yu T, Wang J, Zhang H, Jian Y, Li X, Wang G, Wang G, Hu Y, Lu C, Zhou J, Ma L, Liao M. Genetic characterization of the first Deltacoronavirus from wild birds around Qinghai Lake. Front Microbiol 2024; 15:1423367. [PMID: 38933020 PMCID: PMC11199898 DOI: 10.3389/fmicb.2024.1423367] [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: 04/25/2024] [Accepted: 05/15/2024] [Indexed: 06/28/2024] Open
Abstract
Deltacoronavirus, widely distributed among pigs and wild birds, pose a significant risk of cross-species transmission, including potential human epidemics. Metagenomic analysis of bird samples from Qinghai Lake, China in 2021 reported the presence of Deltacoronavirus. A specific gene fragment of Deltacoronavirus was detected in fecal samples from wild birds at a positive rate of 5.94% (6/101). Next-generation sequencing (NGS) identified a novel Deltacoronavirus strain, which was closely related to isolates from the United Arab Emirates (2018), China (2022), and Poland (2023). Subsequently the strain was named A/black-headed gull/Qinghai/2021(BHG-QH-2021) upon confirmation of the Cytochrome b gene of black-headed gull in the sample. All available genome sequences of avian Deltacoronavirus, including the newly identified BHG-QH-2021 and 5 representative strains of porcine Deltacoronavirus (PDCoV), were classified according to ICTV criteria. In contrast to Coronavirus HKU15, which infects both mammals and birds and shows the possibility of cross-species transmission from bird to mammal host, our analysis revealed that BHG-QH-2021 is classified as Putative species 4. Putative species 4 has been reported to infect 5 species of birds but not mammals, suggesting that cross-species transmission of Putative species 4 is more prevalent among birds. Recombination analysis traced BHG-QH-2021 origin to dut148cor1 and MW01_1o strains, with MW01_1o contributing the S gene. Surprisingly, SwissModle prediction showed that the optimal template for receptor-binding domain (RBD) of BHG-QH-2021 is derived from the human coronavirus 229E, a member of the Alphacoronavirus, rather than the anticipated RBD structure of PDCoV of Deltacoronavirus. Further molecular docking analysis revealed that substituting the loop 1-2 segments of HCoV-229E significantly enhanced the binding capability of BHG-QH-2021 with human Aminopeptidase N (hAPN), surpassing its native receptor-binding domain (RBD). Most importantly, this finding was further confirmed by co-immunoprecipitation experiment that loop 1-2 segments of HCoV-229E enable BHG-QH-2021 RBD binding to hAPN, indicating that the loop 1-2 segment of the RBD in Putative species 4 is a probable key determinant for the virus ability to spill over into humans. Our results summarize the phylogenetic relationships among known Deltacoronavirus, reveal an independent putative avian Deltacoronavirus species with inter-continental and inter-species transmission potential, and underscore the importance of continuous surveillance of wildlife Deltacoronavirus.
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Affiliation(s)
- Ye Tian
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Tianqi Yu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jun Wang
- Animal Husbandry and Veterinary Workstation of the Third Division, Xinjiang Production and Construction Corps, Tumushuke, China
| | - Haoxiang Zhang
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Yingna Jian
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Xiuping Li
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Geping Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Guanghua Wang
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Yong Hu
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Chenhe Lu
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Jiyong Zhou
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
| | - Liqing Ma
- Qinghai Provincial Key Laboratory of Pathogen Diagnosis for Animal Disease and Green Technical Research for Prevention and Control, Qinghai Academy of Animal Sciences and Veterinary Medicine, Qinghai University, Xining, Qinghai, China
| | - Min Liao
- Key Laboratory of Animal Virology, Ministry of Agriculture and Rural Affairs, Zhejiang University, Hangzhou, China
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Falchieri M, Coward VJ, Reid SM, Lewis T, Banyard AC. Infectious bronchitis virus: an overview of the "chicken coronavirus". J Med Microbiol 2024; 73:001828. [PMID: 38771617 PMCID: PMC11184965 DOI: 10.1099/jmm.0.001828] [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: 09/01/2023] [Accepted: 04/05/2024] [Indexed: 05/22/2024] Open
Abstract
Infectious bronchitis virus (IBV) is a highly contagious avian Gammacoronavirus that affects mainly chickens (Gallus gallus) but can circulate in other avian species. IBV constitutes a significant threat to the poultry industry, causing reduced egg yield, growth and mortality levels that can vary in impact. The virus can be transmitted horizontally by inhalation or direct/indirect contact with infected birds or contaminated fomites, vehicles, farm personnel and litter (Figure 1). The error-prone viral polymerase and recombination mechanisms mean diverse viral population results, with multiple genotypes, serotypes, pathotypes and protectotypes. This significantly complicates control and mitigation strategies based on vigilance in biosecurity and the deployment of vaccination.
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Affiliation(s)
- Marco Falchieri
- Avian Virology, Animal and Plant Health Agency (APHA)-Weybridge, Woodham Lane, Addlestone, KT15 3NB, UK
| | - Vivien J. Coward
- Avian Virology, Animal and Plant Health Agency (APHA)-Weybridge, Woodham Lane, Addlestone, KT15 3NB, UK
| | - Scott M. Reid
- Avian Virology, Animal and Plant Health Agency (APHA)-Weybridge, Woodham Lane, Addlestone, KT15 3NB, UK
| | - Tom Lewis
- Avian Virology, Animal and Plant Health Agency (APHA)-Weybridge, Woodham Lane, Addlestone, KT15 3NB, UK
| | - Ashley C. Banyard
- Avian Virology, Animal and Plant Health Agency (APHA)-Weybridge, Woodham Lane, Addlestone, KT15 3NB, UK
- WOAH/FAO International Reference Laboratory for Avian Influenza, Animal and Plant Health Agency (APHA-Weybridge), Woodham Lane, Addlestone, Surrey KT15 3NB, UK
- School of Biological Sciences, University of West Sussex, Falmer, West Sussex, UK
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Kumar A, Tripathi P, Kumar P, Shekhar R, Pathak R. From Detection to Protection: Antibodies and Their Crucial Role in Diagnosing and Combatting SARS-CoV-2. Vaccines (Basel) 2024; 12:459. [PMID: 38793710 PMCID: PMC11125746 DOI: 10.3390/vaccines12050459] [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: 03/13/2024] [Revised: 04/20/2024] [Accepted: 04/22/2024] [Indexed: 05/26/2024] Open
Abstract
Understanding the antibody response to SARS-CoV-2, the virus responsible for COVID-19, is crucial to comprehending disease progression and the significance of vaccine and therapeutic development. The emergence of highly contagious variants poses a significant challenge to humoral immunity, underscoring the necessity of grasping the intricacies of specific antibodies. This review emphasizes the pivotal role of antibodies in shaping immune responses and their implications for diagnosing, preventing, and treating SARS-CoV-2 infection. It delves into the kinetics and characteristics of the antibody response to SARS-CoV-2 and explores current antibody-based diagnostics, discussing their strengths, clinical utility, and limitations. Furthermore, we underscore the therapeutic potential of SARS-CoV-2-specific antibodies, discussing various antibody-based therapies such as monoclonal antibodies, polyclonal antibodies, anti-cytokines, convalescent plasma, and hyperimmunoglobulin-based therapies. Moreover, we offer insights into antibody responses to SARS-CoV-2 vaccines, emphasizing the significance of neutralizing antibodies in order to confer immunity to SARS-CoV-2, along with emerging variants of concern (VOCs) and circulating Omicron subvariants. We also highlight challenges in the field, such as the risks of antibody-dependent enhancement (ADE) for SARS-CoV-2 antibodies, and shed light on the challenges associated with the original antigenic sin (OAS) effect and long COVID. Overall, this review intends to provide valuable insights, which are crucial to advancing sensitive diagnostic tools, identifying efficient antibody-based therapeutics, and developing effective vaccines to combat the evolving threat of SARS-CoV-2 variants on a global scale.
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Affiliation(s)
- Anoop Kumar
- Molecular Diagnostic Laboratory, National Institute of Biologicals, Noida 201309, India
| | - Prajna Tripathi
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, NY 10021, USA;
| | - Prashant Kumar
- R. Ken Coit College of Pharmacy, University of Arizona, Tucson, AZ 85721, USA
| | - Ritu Shekhar
- Department of Molecular Genetics and Microbiology, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Rajiv Pathak
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
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5
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Ford CE, Dunn CD, Leis EM, Thiel WA, Goldberg TL. Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes. Pathogens 2024; 13:150. [PMID: 38392888 PMCID: PMC10891596 DOI: 10.3390/pathogens13020150] [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: 12/18/2023] [Revised: 02/01/2024] [Accepted: 02/05/2024] [Indexed: 02/25/2024] Open
Abstract
Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.
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Affiliation(s)
- Charlotte E. Ford
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
| | - Christopher D. Dunn
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
| | - Eric M. Leis
- U.S. Fish and Wildlife Service, La Crosse Fish Health Center—Midwest Fisheries Center, Onalaska, WI 54650, USA;
| | - Whitney A. Thiel
- Robert P. Hanson Laboratories, University of Wisconsin-Madison, Madison, WI 53706, USA;
| | - Tony L. Goldberg
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA; (C.E.F.); (C.D.D.)
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Shaprova ON, Shanshin DV, Kolosova EA, Borisevich SS, Soroka AA, Merkuleva IA, Nikitin AO, Volosnikova EA, Ushkalenko ND, Zaykovskaya AV, Pyankov OV, Elchaninova SA, Shcherbakov DN, Ilyicheva TN. Pre-Pandemic Cross-Reactive Immunity against SARS-CoV-2 among Siberian Populations. Antibodies (Basel) 2023; 12:82. [PMID: 38131804 PMCID: PMC10741209 DOI: 10.3390/antib12040082] [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: 09/28/2023] [Revised: 11/20/2023] [Accepted: 12/01/2023] [Indexed: 12/23/2023] Open
Abstract
In December 2019, a new coronavirus, SARS-CoV-2, was found to in Wuhan, China. Cases of infection were subsequently detected in other countries in a short period of time, resulting in the declaration of the COVID-19 pandemic by the World Health Organization (WHO) on 11 March 2020. Questions about the impact of herd immunity of pre-existing immune reactivity to SARS-CoV-2 on COVID-19 severity, associated with the immunity to seasonal manifestation, are still to be resolved and may be useful for understanding some processes that precede the emergence of a pandemic virus. Perhaps this will contribute to understanding some of the processes that precede the emergence of a pandemic virus. We assessed the specificity and virus-neutralizing capacity of antibodies reacting with the nucleocapsid and spike proteins of SARS-CoV-2 in a set of serum samples collected in October and November 2019, before the first COVID-19 cases were documented in this region. Blood serum samples from 799 residents of several regions of Siberia, Russia, (the Altai Territory, Irkutsk, Kemerovo and Novosibirsk regions, the Republic of Altai, Buryatia, and Khakassia) were analyzed. Sera of non-infected donors were collected within a study of seasonal influenza in the Russian Federation. The sample collection sites were located near the flyways and breeding grounds of wild waterfowl. The performance of enzyme-linked immunosorbent assay (ELISA) for the collected sera included the usage of recombinant SARS-CoV-2 protein antigens: full-length nucleocapsid protein (CoVN), receptor binding domain (RBD) of S-protein and infection fragment of the S protein (S5-6). There were 183 (22.9%) sera reactive to the S5-6, 270 (33.8%) sera corresponding to the full-length N protein and 128 (16.2%) sera simultaneously reactive to both these proteins. Only 5 out of 799 sera had IgG antibodies reactive to the RBD. None of the sera exhibited neutralizing activity against the nCoV/Victoria/1/2020 SARS-CoV-2 strain in Vero E6 cell culture. The data obtained in this study suggest that some of the population of the analyzed regions of Russia had cross-reactive humoral immunity against SARS-CoV-2 before the COVID-19 pandemic started. Moreover, among individuals from relatively isolated regions, there were significantly fewer reliably cross-reactive sera. The possible significance of these data and impact of cross-immunity to SARS-CoV-2 on the prevalence and mortality of COVID-19 needs further assessment.
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Affiliation(s)
- Olga N. Shaprova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Daniil V. Shanshin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Evgeniia A. Kolosova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Sophia S. Borisevich
- Laboratory of Chemical Physics, Ufa Institute of Chemistry Ufa Federal Research Center, 450078 Ufa, Russia;
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Artem A. Soroka
- Institute of Intelligent Cybernetic Systems, National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), 115409 Moscow, Russia;
| | - Iuliia A. Merkuleva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Artem O. Nikitin
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Ekaterina A. Volosnikova
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Nikita D. Ushkalenko
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Anna V. Zaykovskaya
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Oleg V. Pyankov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
| | - Svetlana A. Elchaninova
- Department of Biochemistry and Clinical Laboratory Diagnostics, Altai State Medical University, 656038 Barnaul, Russia;
| | - Dmitry N. Shcherbakov
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
- Russian-American Anti-Cancer Center, Altai State University, 656049 Barnaul, Russia
| | - Tatiana N. Ilyicheva
- State Research Center of Virology and Biotechnology VECTOR, Rospotrebnadzor, 630559 Koltsovo, Russia; (O.N.S.); (D.V.S.); (I.A.M.); (A.O.N.); (E.A.V.); (N.D.U.); (A.V.Z.); (O.V.P.); (D.N.S.); (T.N.I.)
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Domańska-Blicharz K, Miłek-Krupa J, Pikuła A. Gulls as a host for both gamma and deltacoronaviruses. Sci Rep 2023; 13:15104. [PMID: 37704675 PMCID: PMC10499781 DOI: 10.1038/s41598-023-42241-8] [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: 03/28/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023] Open
Abstract
The coronaviruses (CoV) are ubiquitous pathogens found in wide variety of hosts that constantly pose a threat to human and animal health as a result of their enormous capacity to generate genetic changes. Constant monitoring of virus reservoirs can constitute an early-warning tool and control the spread and evolution of the virus. Coronaviruses are common in wild birds, globally, and birds of the Charadriiformes in particular have been demonstrated to be carriers of delta- (dCoV) and gammacoronaviruses (gCoV). In this paper, we present the genetic characterisation of five CoV strains from black-headed (Chroicocephalus ridibundus) and common (Larus canus) gulls. Whole genome sequence analysis showed high similarity of detected dCoV in gulls to previously identified strains from falcon, houbara, pigeon and gulls from Asia (UAE, China). However, phylogenetic analysis revealed bifurcation within a common branch. Furthermore, the accumulation of numerous amino acid changes within the S-protein was demonstrated, indicating further evolution of dCoV within a single gull host. In turn, phylogenetic analysis for the most of the structural and non-structural genes of identified gCoV confirmed that the strain belongs to the duck coronavirus 2714 (DuCoV2714) species within Igacovirus subgenera, while for the spike protein it forms a separate branch not closely related to any gCoV species known to date. The current study provides new and significant insights into the evolution and diversification of circulating coronaviruses in members of Laridae family.
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Affiliation(s)
- Katarzyna Domańska-Blicharz
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland.
| | - Justyna Miłek-Krupa
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
- Holy Cross Cancer Center, Stefana Artwińskiego 3, 25-734, Kielce, Poland
| | - Anna Pikuła
- Department of Poultry Diseases, National Veterinary Research Institute, al. Partyzantow 57, 24-100, Pulawy, Poland
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Chattopadhyay A, Jailani AAK, Mandal B. Exigency of Plant-Based Vaccine against COVID-19 Emergence as Pandemic Preparedness. Vaccines (Basel) 2023; 11:1347. [PMID: 37631915 PMCID: PMC10458178 DOI: 10.3390/vaccines11081347] [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: 06/20/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
After two years since the declaration of COVID-19 as a pandemic by the World Health Organization (WHO), more than six million deaths have occurred due to SARS-CoV-2, leading to an unprecedented disruption of the global economy. Fortunately, within a year, a wide range of vaccines, including pathogen-based inactivated and live-attenuated vaccines, replicating and non-replicating vector-based vaccines, nucleic acid (DNA and mRNA)-based vaccines, and protein-based subunit and virus-like particle (VLP)-based vaccines, have been developed to mitigate the severe impacts of the COVID-19 pandemic. These vaccines have proven highly effective in reducing the severity of illness and preventing deaths. However, the availability and supply of COVID-19 vaccines have become an issue due to the prioritization of vaccine distribution in most countries. Additionally, as the virus continues to mutate and spread, questions have arisen regarding the effectiveness of vaccines against new strains of SARS-CoV-2 that can evade host immunity. The urgent need for booster doses to enhance immunity has been recognized. The scarcity of "safe and effective" vaccines has exacerbated global inequalities in terms of vaccine coverage. The development of COVID-19 vaccines has fallen short of the expectations set forth in 2020 and 2021. Furthermore, the equitable distribution of vaccines at the global and national levels remains a challenge, particularly in developing countries. In such circumstances, the exigency of plant virus-based vaccines has become apparent as a means to overcome supply shortages through fast manufacturing processes and to enable quick and convenient distribution to millions of people without the reliance on a cold chain system. Moreover, plant virus-based vaccines have demonstrated both safety and efficacy in eliciting robust cellular immunogenicity against COVID-19 pathogens. This review aims to shed light on the advantages and disadvantages of different types of vaccines developed against SARS-CoV-2 and provide an update on the current status of plant-based vaccines in the fight against the COVID-19 pandemic.
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Affiliation(s)
- Anirudha Chattopadhyay
- Pulses Research Station, Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar 385506, India;
| | - A. Abdul Kader Jailani
- Department of Plant Pathology, North Florida Research and Education Center, University of Florida, Quincy, FL 32351, USA
| | - Bikash Mandal
- Advanced Centre for Plant Virology, Division of Plant Pathology, Indian Agricultural Research Institute, New Delhi 110012, India
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Sharshov K, Dubovitskiy N, Derko A, Loginova A, Kolotygin I, Zhirov D, Sobolev I, Kurskaya O, Alekseev A, Druzyaka A, Ktitorov P, Kulikova O, He G, Wang Z, Bi Y, Shestopalov A. Does Avian Coronavirus Co-Circulate with Avian Paramyxovirus and Avian Influenza Virus in Wild Ducks in Siberia? Viruses 2023; 15:v15051121. [PMID: 37243207 DOI: 10.3390/v15051121] [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: 05/04/2023] [Accepted: 05/05/2023] [Indexed: 05/28/2023] Open
Abstract
Avian coronaviruses (ACoV) have been shown to be highly prevalent in wild bird populations. More work on avian coronavirus detection and diversity estimation is needed for the breeding territories of migrating birds, where the high diversity and high prevalence of Orthomyxoviridae and Paramyxoviridae have already been shown in wild birds. In order to detect ACoV RNA, we conducted PCR diagnostics of cloacal swab samples from birds, which we monitored during avian influenza A virus surveillance activities. Samples from two distant Asian regions of Russia (Sakhalin region and Novosibirsk region) were tested. Amplified fragments of the RNA-dependent RNA-polymerase (RdRp) of positive samples were partially sequenced to determine the species of Coronaviridae represented. The study revealed a high presence of ACoV among wild birds in Russia. Moreover, there was a high presence of birds co-infected with avian coronavirus, avian influenza virus, and avian paramyxovirus. We found one case of triple co-infection in a Northern Pintail (Anas acuta). Phylogenetic analysis revealed the circulation of a Gammacoronavirus species. A Deltacoronavirus species was not detected, which supports the data regarding the low prevalence of deltacoronaviruses among surveyed bird species.
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Affiliation(s)
- Kirill Sharshov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Nikita Dubovitskiy
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Anastasiya Derko
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Arina Loginova
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Ilya Kolotygin
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
| | - Dmitry Zhirov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
- Faculty of Natural Sciences, Novosibirsk State University, Novosibirsk 630073, Russia
| | - Ivan Sobolev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Olga Kurskaya
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexander Alekseev
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
| | - Alexey Druzyaka
- Institute of Animal Systematics and Ecology, Novosibirsk 630091, Russia
| | - Pavel Ktitorov
- Institute of Biological Problems of the North, Magadan 685000, Russia
| | - Olga Kulikova
- Institute of Biological Problems of the North, Magadan 685000, Russia
| | - Guimei He
- School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Zhenghuan Wang
- School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Yuhai Bi
- Center for Influenza Research and Early-warning (CASCIRE), CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Alexander Shestopalov
- Federal Research Center of Fundamental and Translational Medicine, Novosibirsk 630117, Russia
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