1
|
Park ES, Kuroda Y, Uda A, Kaku Y, Okutani A, Hotta A, Tatemoto K, Ishijima K, Inoue Y, Harada M, Ami Y, Shirakura M, Watanabe S, Suzuki Y, Harada T, Ainai A, Shiwa N, Sakai Y, Iwata-Yoshikawa N, Nagata N, Suzuki T, Hasegawa H, Maeda K. The comparison of pathogenicity among SARS-CoV-2 variants in domestic cats. Sci Rep 2024; 14:21815. [PMID: 39294189 PMCID: PMC11410826 DOI: 10.1038/s41598-024-71791-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 08/30/2024] [Indexed: 09/20/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been detected or isolated from domestic cats. It is unclear whether cats play an important role in the SARS-CoV-2 transmission cycle. In this study, we examined the susceptibility of cats to SARS-CoV-2, including wild type and variants, by animal experiments. Cats inoculated with wild type, gamma, and delta variants secreted a large amount of SARS-CoV-2 for 1 week after the inoculation from nasal, oropharyngeal, and rectal routes. Only 100 TCID50 of virus could infect cats and replicate well without severe clinical symptoms. In addition, one cat inoculated with wild type showed persistent virus secretion in feces for over 28 days post-inoculation (dpi). The titer of virus-neutralizing (VN) antibodies against SARS-CoV-2 increased from 11 dpi, reaching a peak at 14 dpi. However, the omicron variant could not replicate well in cat tissues and induced a lower titer of VN antibodies. It is concluded that cats were highly susceptible to SARS-CoV-2 infection, but not to the Omicron Variant, which caused the attenuated pathogenicity.
Collapse
Affiliation(s)
- Eun-Sil Park
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yudai Kuroda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Akihiko Uda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yoshihiro Kaku
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Akiko Okutani
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Akitoyo Hotta
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Kango Tatemoto
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Keita Ishijima
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yusuke Inoue
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Michiko Harada
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, 753-8515, Japan
| | - Yasushi Ami
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Masayuki Shirakura
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Musashimurayama, 208-0011, Japan
| | - Shinji Watanabe
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Musashimurayama, 208-0011, Japan
| | - Yasushi Suzuki
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Musashimurayama, 208-0011, Japan
| | - Toshihiko Harada
- Research Center for Biosafety, Laboratory Animal, and Pathogen Bank, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Akira Ainai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Nozomi Shiwa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yusuke Sakai
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Naoko Iwata-Yoshikawa
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Noriyo Nagata
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Tadaki Suzuki
- Department of Pathology, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Hideki Hasegawa
- Research Center for Influenza and Respiratory Viruses, National Institute of Infectious Diseases, Musashimurayama, 208-0011, Japan
| | - Ken Maeda
- Department of Veterinary Science, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
- Joint Graduate School of Veterinary Science, Yamaguchi University, Yamaguchi, 753-8515, Japan.
| |
Collapse
|
2
|
Fauziah I, Nugroho HA, Yanthi ND, Tiffarent R, Saputra S. Potential zoonotic spillover at the human-animal interface: A mini-review. Vet World 2024; 17:289-302. [PMID: 38595670 PMCID: PMC11000462 DOI: 10.14202/vetworld.2024.289-302] [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: 10/02/2023] [Accepted: 01/09/2024] [Indexed: 04/11/2024] Open
Abstract
Wildlife markets and wet wildlife markets, a type of human-animal interface, are commonly trading centers for wild-caught and captive-exotic animals as well as their products. These markets provide an ideal environment for spillovers of zoonotic and emerging infectious diseases (EIDs). These conditions may raise serious concerns, particularly in relation to wildlife species that frequently interact with humans and domestic animals. EIDs pose a significant risk to humans, ecosystems, and public health, as demonstrated by the current COVID-19 pandemic, and other previous outbreaks, including the highly pathogenic avian influenza H5N1. Even though it seems appears impossible to eliminate EIDs, we may still be able to minimalize the risks and take several measures to prevent new EIDs originated from animals. The aim of this study was to review several types of human-animal interfaces with a high risk of zoonotic spillover, infectious agents, and animal hosts or reservoirs. Identifying those factors will support the development of interventions and effective disease control in human-animal interface settings.
Collapse
Affiliation(s)
- Ima Fauziah
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Herjuno Ari Nugroho
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Nova Dilla Yanthi
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Rida Tiffarent
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| | - Sugiyono Saputra
- Research Center for Applied Microbiology, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), KST Soekarno, Jalan Raya Jakarta Bogor Km 46 Cibinong, Bogor, West Java, Indonesia
| |
Collapse
|
3
|
Townsend JP, Hassler HB, Lamb AD, Sah P, Alvarez Nishio A, Nguyen C, Tew AD, Galvani AP, Dornburg A. Seasonality of endemic COVID-19. mBio 2023; 14:e0142623. [PMID: 37937979 PMCID: PMC10746271 DOI: 10.1128/mbio.01426-23] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023] Open
Abstract
IMPORTANCE The seasonality of COVID-19 is important for effective healthcare and public health decision-making. Previous waves of SARS-CoV-2 infections have indicated that the virus will likely persist as an endemic pathogen with distinct surges. However, the timing and patterns of potentially seasonal surges remain uncertain, rendering effective public health policies uninformed and in danger of poorly anticipating opportunities for intervention, such as well-timed booster vaccination drives. Applying an evolutionary approach to long-term data on closely related circulating coronaviruses, our research provides projections of seasonal surges that should be expected at major temperate population centers. These projections enable local public health efforts that are tailored to expected surges at specific locales or regions. This knowledge is crucial for enhancing medical preparedness and facilitating the implementation of targeted public health interventions.
Collapse
Affiliation(s)
- Jeffrey P. Townsend
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, USA
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, USA
- Program in Microbiology, Yale University, New Haven, USA
| | - Hayley B. Hassler
- Department of Biostatistics, Yale School of Public Health, New Haven, USA
| | - April D. Lamb
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Pratha Sah
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | | | - Cameron Nguyen
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alexandra D. Tew
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| | - Alison P. Galvani
- Center for Infectious Disease Modeling and Analysis, Yale University, New Haven, USA
| | - Alex Dornburg
- Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, USA
| |
Collapse
|
4
|
Hadizadeh N, Naderi M, Khezri J, Yazdani M, Shamsara M, Hashemi E. Appraisal of SARS-CoV-2 mutations and their impact on vaccination efficacy: an overview. J Diabetes Metab Disord 2022; 21:1763-1783. [PMID: 35891981 PMCID: PMC9305048 DOI: 10.1007/s40200-022-01002-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 02/07/2022] [Indexed: 12/02/2022]
Abstract
With the unexpected emergence of the novel 2019 Wuhan coronavirus, the world was faced with a sudden uproar that quickly shifted into a serious life-threatening pandemic. Affecting the lives of the global population and leaving drastic damage in various sections and systems, several measures have been constantly taken to tackle down this crisis. For instance, numerous vaccines have been developed in the past two years, some of which have been granted emergency use, thus providing sufficient immunity to the vaccinated individuals. However, the appearance of newly emerged SARS-CoV-2 variants with accelerated transmission and fatality has led the world towards another pandemic. Having undergone various mutations in genomic and/or amino acid profiles, some of the emerged variants of concern (VOCs) including Alpha, Beta, Gamma, and Delta have displayed immune evasion and pathogenicity even in the vaccinated population, hence raising concerns regarding the efficacy of current vaccines against new VOCs of COVID-19. Therefore, genomic investigations of SARS-CoV-2 mutations are expected to provide valuable insight into the evolution of SARS-CoV-2, while also determining the impact of different mutations on infection severity. This study was constructed with the aim of shining light on recent advances regarding mutations in major COVID-19 VOCs, as well as vaccination efficacy against those VOCs.
Collapse
Affiliation(s)
- Nastaran Hadizadeh
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Mousa Naderi
- Metabolic Disorders Research Center, Endocrinology and Metabolism Molecular -Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-16, Tehran, Iran
| | - Jafar Khezri
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-16, Tehran, Iran
| | - Meysam Yazdani
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-16, Tehran, Iran
| | - Mehdi Shamsara
- Department of Animal Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-16, Tehran, Iran
- National Research Centre for Transgenic Mouse, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-161, Tehran, Iran
| | - Ehsan Hashemi
- Diabetes Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
- National Research Centre for Transgenic Mouse, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 14965-161, Tehran, Iran
| |
Collapse
|
5
|
COVID-19: A Veterinary and One Health Perspective. J Indian Inst Sci 2022; 102:689-709. [PMID: 35968231 PMCID: PMC9364302 DOI: 10.1007/s41745-022-00318-9] [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: 11/27/2021] [Accepted: 06/21/2022] [Indexed: 10/30/2022]
Abstract
Interface with animals has been responsible for the occurrence of a major proportion of human diseases for the past several decades. Recent outbreaks of respiratory, haemorrhagic, encephalitic, arthropod-borne and other viral diseases have underlined the role of animals in the transmission of pathogens to humans. The on-going coronavirus disease-2019 (COVID-19) pandemic is one among them and is thought to have originated from bats and jumped to humans through an intermediate animal host. Indeed, the aetiology, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can infect and cause disease in cats, ferrets and minks, as well as be transmitted from one animal to another. The seriousness of the pandemic along with the zoonotic origin of the virus has been a red alert on the critical need for collaboration and cooperation among human and animal health professionals, as well as stakeholders from various other disciplines that study planetary health parameters and the well-being of the biosphere. It is therefore imminent that One Health principles are applied across the board for human infectious diseases so that we can be better prepared for future zoonotic disease outbreaks and pandemics.
Collapse
|
6
|
Valdebenito S, Bessis S, Annane D, Lorin de la Grandmaison G, Cramer–Bordé E, Prideaux B, Eugenin EA, Bomsel M. COVID-19 Lung Pathogenesis in SARS-CoV-2 Autopsy Cases. Front Immunol 2021; 12:735922. [PMID: 34671353 PMCID: PMC8521087 DOI: 10.3389/fimmu.2021.735922] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 09/06/2021] [Indexed: 12/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major public health issue. COVID-19 is considered an airway/multi-systemic disease, and demise has been associated with an uncontrolled immune response and a cytokine storm in response to the virus. However, the lung pathology, immune response, and tissue damage associated with COVID-19 demise are poorly described and understood due to safety concerns. Using post-mortem lung tissues from uninfected and COVID-19 deadly cases as well as an unbiased combined analysis of histology, multi-viral and host markers staining, correlative microscopy, confocal, and image analysis, we identified three distinct phenotypes of COVID-19-induced lung damage. First, a COVID-19-induced hemorrhage characterized by minimal immune infiltration and large thrombus; Second, a COVID-19-induced immune infiltration with excessive immune cell infiltration but no hemorrhagic events. The third phenotype correspond to the combination of the two previous ones. We observed the loss of alveolar wall integrity, detachment of lung tissue pieces, fibroblast proliferation, and extensive fibrosis in all three phenotypes. Although lung tissues studied were from lethal COVID-19, a strong immune response was observed in all cases analyzed with significant B cell and poor T cell infiltrations, suggesting an exhausted or compromised immune cellular response in these patients. Overall, our data show that SARS-CoV-2-induced lung damage is highly heterogeneous. These individual differences need to be considered to understand the acute and long-term COVID-19 consequences.
Collapse
Affiliation(s)
- Silvana Valdebenito
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Simon Bessis
- Service des Maladies Infectieuses, Centre Hospitalier Universitaire Raymond Poincaré, AP-HP, Garches, France
| | - Djillali Annane
- Intensive Care Unit, Raymond Poincaré Hospital (AP-HP), Paris, France
- Simone Veil School of Medicine, Université of Versailles, Versailles, France
- University Paris Saclay, Garches, France
| | - Geoffroy Lorin de la Grandmaison
- Department of Forensic Medicine and Pathology, Versailles Saint-Quentin Université, AP-HP, Raymond Poincaré Hospital, Garches, France
| | | | - Brendan Prideaux
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Eliseo A. Eugenin
- Department of Neuroscience, Cell Biology and Anatomy, University of Texas Medical Branch (UTMB), Galveston, TX, United States
| | - Morgane Bomsel
- Laboratory of Mucosal Entry of HIV-1 and Mucosal Immunity, Department of Infection, Immunity, and Inflammation, Institute Cochin, CNRS UMR 8104, INSERM U1016, University of Paris, Paris, France
| |
Collapse
|
7
|
Engineered receptor binding domain immunogens elicit pan-sarbecovirus neutralizing antibodies outside the receptor binding motif. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33330872 DOI: 10.1101/2020.12.07.415216] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Effective countermeasures are needed against emerging coronaviruses of pandemic potential, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Designing immunogens that elicit broadly neutralizing antibodies to conserved viral epitopes on the major surface glycoprotein, spike, such as the receptor binding domain (RBD) is one potential approach. Here, we report the generation of homotrimeric RBD immunogens from different sarbecoviruses using a stabilized, immune-silent trimerization tag. In mice, we find that a cocktail of these homotrimeric sarbecovirus RBDs elicits antibodies to conserved viral epitopes outside of the ACE2 receptor binding motif (RBM). Importantly, these responses neutralize all sarbecovirus components even in context of prior SARS-CoV-2 imprinting. We further show that a substantial fraction of the neutralizing antibodies elicited after vaccination in humans also engages non-RBM epitopes on the RBD. Collectively, our results suggest a strategy for eliciting broadly neutralizing responses leading to a pan-sarbecovirus vaccine. Author summary Immunity to SARS-CoV-2 in the human population will be widespread due to natural infection and vaccination. However, another novel coronavirus will likely emerge in the future and may cause a subsequent pandemic. Humoral responses induced by SARS-CoV-2 infection and vaccination provide limited protection against even closely related coronaviruses. We show immunization with a cocktail of trimeric coronavirus receptor binding domains induces a neutralizing antibody response that is broadened to related coronaviruses with pandemic potential. Importantly, this broadening occurs in context of an initial imprinted SARS-CoV-2 spike immunization showing that preexisting immunity can be expanded to recognize other related coronaviruses. Our immunogens focused the serum antibody response to conserved epitopes on the receptor binding domain outside of the ACE2 receptor binding motif; this contrasts with current SARS-CoV-2 therapeutic antibodies, which predominantly target the receptor binding motif.
Collapse
|
8
|
Ecology and Evolution of Betacoronaviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:41-60. [PMID: 33973171 DOI: 10.1007/978-3-030-63761-3_3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The crown-like outline of the virions of coronaviruses will long endure as the iconic image of 2020 - the year of the COVID-19 pandemic. This major human health emergency has been caused by a betacoronavirus, as have others in the past. In this chapter, we outline the taxonomy of betacoronaviruses and their properties, both genetic and biological. We discuss their recombinational and mutational histories separately to show that the sequence of the RaTG13 bat virus isolate is the closest currently known full-length genetic homolog of that of the severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2). However, the RaTG13 bat virus and SARS-CoV-2 have probably diverged over 20 years. We discuss the ecology of their pangolin and bat hosts and conclude that, like other recent viral pandemics, the underlying cause of the SARS-CoV-2 emergence is probably the relentless growth of the world's human population and the overexploitation and disturbance of the environment.
Collapse
|
9
|
Godoy MG, Kibenge MJT, Kibenge FSB. SARS-CoV-2 transmission via aquatic food animal species or their products: A review. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 536:736460. [PMID: 33564203 PMCID: PMC7860939 DOI: 10.1016/j.aquaculture.2021.736460] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 05/06/2023]
Abstract
Outbreaks of COVID-19 (coronavirus disease 2019) have been reported in workers in fish farms and fish processing plants arising from person-to-person transmission, raising concerns about aquatic animal food products' safety. A better understanding of such incidents is important for the aquaculture industry's sustainability, particularly with the global trade in fresh and frozen aquatic animal food products where contaminating virus could survive for some time. Despite a plethora of COVID-19-related scientific publications, there is a lack of reports on the risk of contact with aquatic food animal species or their products. This review aimed to examine the potential for Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) contamination and the potential transmission via aquatic food animals or their products and wastewater effluents. The extracellular viability of SARS-CoV-2 and how the virus is spread are reviewed, supporting the understanding that contaminated cold-chain food sources may introduce SAR-CoV-2 via food imports although the virus is unlikely to infect humans through consumption of aquatic food animals or their products or drinking water; i.e., SARS-CoV-2 is not a foodborne virus and should not be managed as such but instead through strong, multifaceted public health interventions including physical distancing, rapid contact tracing, and testing, enhanced hand and respiratory hygiene, frequent disinfection of high-touch surfaces, isolation of infected workers and their contacts, as well as enhanced screening protocols for international seafood trade.
Collapse
Affiliation(s)
- Marcos G Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Lago Panguipulli 1390, Puerto Montt, Chile
- Laboratorio de Biotecnología Aplicada, Facultad de Medicina Veterinaria, Sede De La Patagonia, Lago Panguipulli 1390, Puerto Montt, 5480000, Chile
- Doctorado en Acuicultura. Programa Cooperativo Universidad de Chile, Universidad Católica del Norte, Pontificia Universidad Católica de Valparaíso, Chile
| | - Molly J T Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
| | - Frederick S B Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave., Charlottetown, P.E.I., C1A 4P3, Canada
| |
Collapse
|
10
|
Vasilarou M, Alachiotis N, Garefalaki J, Beloukas A, Pavlidis P. Population Genomics Insights into the First Wave of COVID-19. Life (Basel) 2021; 11:129. [PMID: 33562321 PMCID: PMC7914631 DOI: 10.3390/life11020129] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/30/2021] [Accepted: 02/04/2021] [Indexed: 01/09/2023] Open
Abstract
Full-genome-sequence computational analyses of the SARS-coronavirus (CoV)-2 genomes allow us to understand the evolutionary events and adaptability mechanisms. We used population genetics analyses on human SARS-CoV-2 genomes available on 2 April 2020 to infer the mutation rate and plausible recombination events between the Betacoronavirus genomes in nonhuman hosts that may have contributed to the evolution of SARS-CoV-2. Furthermore, we localized the targets of recent and strong, positive selection during the first pandemic wave. The genomic regions that appear to be under positive selection are largely co-localized with regions in which recombination from nonhuman hosts took place. Our results suggest that the pangolin coronavirus genome may have contributed to the SARS-CoV-2 genome by recombination with the bat coronavirus genome. However, we find evidence for additional recombination events that involve coronavirus genomes from other hosts, i.e., hedgehogs and sparrows. We further infer that recombination may have recently occurred within human hosts. Finally, we estimate the parameters of a demographic scenario involving an exponential growth of the size of the SARS-CoV-2 populations that have infected European, Asian, and Northern American cohorts, and we demonstrate that a rapid exponential growth in population size from the first wave can support the observed polymorphism patterns in SARS-CoV-2 genomes.
Collapse
Affiliation(s)
- Maria Vasilarou
- Foundation for Research and Technology Hellas (FORTH) and Department of Biology, Institute of Molecular Biology and Biotechnology (IMBB), University of Crete, 70013 Crete, Greece;
| | | | - Joanna Garefalaki
- Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece;
| | - Apostolos Beloukas
- Department of Biomedical Sciences, University of West Attica, 12243 Athens, Greece
- Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7BE, UK
| | - Pavlos Pavlidis
- Institute of Computer Science (ICS), Foundation for Research and Technology Hellas (FORTH), 70013 Heraklion, Greece;
| |
Collapse
|
11
|
Makarenkov V, Mazoure B, Rabusseau G, Legendre P. Horizontal gene transfer and recombination analysis of SARS-CoV-2 genes helps discover its close relatives and shed light on its origin. BMC Ecol Evol 2021; 21:5. [PMID: 33514319 PMCID: PMC7817968 DOI: 10.1186/s12862-020-01732-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic is one of the greatest global medical and social challenges that have emerged in recent history. Human coronavirus strains discovered during previous SARS outbreaks have been hypothesized to pass from bats to humans using intermediate hosts, e.g. civets for SARS-CoV and camels for MERS-CoV. The discovery of an intermediate host of SARS-CoV-2 and the identification of specific mechanism of its emergence in humans are topics of primary evolutionary importance. In this study we investigate the evolutionary patterns of 11 main genes of SARS-CoV-2. Previous studies suggested that the genome of SARS-CoV-2 is highly similar to the horseshoe bat coronavirus RaTG13 for most of the genes and to some Malayan pangolin coronavirus (CoV) strains for the receptor binding (RB) domain of the spike protein. RESULTS We provide a detailed list of statistically significant horizontal gene transfer and recombination events (both intergenic and intragenic) inferred for each of 11 main genes of the SARS-CoV-2 genome. Our analysis reveals that two continuous regions of genes S and N of SARS-CoV-2 may result from intragenic recombination between RaTG13 and Guangdong (GD) Pangolin CoVs. Statistically significant gene transfer-recombination events between RaTG13 and GD Pangolin CoV have been identified in region [1215-1425] of gene S and region [534-727] of gene N. Moreover, some statistically significant recombination events between the ancestors of SARS-CoV-2, RaTG13, GD Pangolin CoV and bat CoV ZC45-ZXC21 coronaviruses have been identified in genes ORF1ab, S, ORF3a, ORF7a, ORF8 and N. Furthermore, topology-based clustering of gene trees inferred for 25 CoV organisms revealed a three-way evolution of coronavirus genes, with gene phylogenies of ORF1ab, S and N forming the first cluster, gene phylogenies of ORF3a, E, M, ORF6, ORF7a, ORF7b and ORF8 forming the second cluster, and phylogeny of gene ORF10 forming the third cluster. CONCLUSIONS The results of our horizontal gene transfer and recombination analysis suggest that SARS-CoV-2 could not only be a chimera virus resulting from recombination of the bat RaTG13 and Guangdong pangolin coronaviruses but also a close relative of the bat CoV ZC45 and ZXC21 strains. They also indicate that a GD pangolin may be an intermediate host of this dangerous virus.
Collapse
Affiliation(s)
- Vladimir Makarenkov
- Département d'informatique, Université du Québec à Montréal, Montreal, QC, Canada.
| | - Bogdan Mazoure
- Montreal Institute for Learning Algorithms (Mila), Montreal, QC, Canada
| | - Guillaume Rabusseau
- Montreal Institute for Learning Algorithms (Mila), Montreal, QC, Canada
- Département d'informatique et de Recherche Opérationnelle, Université de Montréal and Canada CIFAR AI Chair, Montreal, QC, Canada
| | - Pierre Legendre
- Département de Sciences Biologiques, Université de Montréal, C. P. 6128, Succursale Centre-Ville, Montreal, QC, H3C 3J7, Canada
| |
Collapse
|
12
|
Fahmi M, Kharisma VD, Ansori ANM, Ito M. Retrieval and Investigation of Data on SARS-CoV-2 and COVID-19 Using Bioinformatics Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1318:839-857. [PMID: 33973215 DOI: 10.1007/978-3-030-63761-3_47] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Sudden emergence and a rapid outbreak of SARS-CoV-2 accompanied by a devastating impact on the economy and public health has driven extensive scientific mobilization to study and elucidate the various associated concerns about SARS-CoV-2. Bioinformatics plays a crucial role in addressing and providing solutions to questions about SARS-CoV-2. It helps shorten the duration for the vaccine development process and the discovery of potential clinical interventions through the simulation and information retrieval, and the development of well-ordered information hubs and resources, which are essential to derive data and meaningful findings from the current massive information about SARS-CoV-2. Advanced algorithms in this field also provide approaches that are essential to elucidate the relationship, origin, and evolutionary process of SARS-CoV-2. Here, we report essential bioinformatics entities, such as database and platform development, molecular evolution and phylogenetic analyses, and vaccine designs, that are useful to solve the SARS-CoV-2 conundrum.
Collapse
Affiliation(s)
- Muhamad Fahmi
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan
| | - Viol Dhea Kharisma
- Master Program in Biology, Department of Biology, Faculty of Mathematic and Natural Sciences, Universitas Brawijaya, Malang, Indonesia.,Computational Virology and Complexity Science Research Unit, Division of Molecular Biology and Genetics, Generasi Biologi Indonesia (GENBINESIA) Foundation, Gresik, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Malang, Indonesia
| | - Arif Nur Muhammad Ansori
- Doctoral Program in Veterinary Science, Faculty of Veterinary Medicine, Universitas Airlangga, Kampus C Universitas Airlangga, Surabaya, Indonesia.,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Surabaya, Indonesia
| | - Masahiro Ito
- Advanced Life Sciences Program, Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, Japan. .,Systematic Review and Meta-analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Kusatsu, Japan.
| |
Collapse
|
13
|
Li T, Liu D, Yang Y, Guo J, Feng Y, Zhang X, Cheng S, Feng J. Phylogenetic supertree reveals detailed evolution of SARS-CoV-2. Sci Rep 2020; 10:22366. [PMID: 33353955 PMCID: PMC7755913 DOI: 10.1038/s41598-020-79484-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Accepted: 12/09/2020] [Indexed: 02/06/2023] Open
Abstract
Corona Virus Disease 2019 (COVID-19) caused by the emerged coronavirus SARS-CoV-2 is spreading globally. The origin of SARS-Cov-2 and its evolutionary relationship is still ambiguous. Several reports attempted to figure out this critical issue by genome-based phylogenetic analysis, yet limited progress was obtained, principally owing to the disability of these methods to reasonably integrate phylogenetic information from all genes of SARS-CoV-2. Supertree method based on multiple trees can produce the overall reasonable phylogenetic tree. However, the supertree method has been barely used for phylogenetic analysis of viruses. Here we applied the matrix representation with parsimony (MRP) pseudo-sequence supertree analysis to study the origin and evolution of SARS-CoV-2. Compared with other phylogenetic analysis methods, the supertree method showed more resolution power for phylogenetic analysis of coronaviruses. In particular, the MRP pseudo-sequence supertree analysis firmly disputes bat coronavirus RaTG13 be the last common ancestor of SARS-CoV-2, which was implied by other phylogenetic tree analysis based on viral genome sequences. Furthermore, the discovery of evolution and mutation in SARS-CoV-2 was achieved by MRP pseudo-sequence supertree analysis. Taken together, the MRP pseudo-sequence supertree provided more information on the SARS-CoV-2 evolution inference relative to the normal phylogenetic tree based on full-length genomic sequences.
Collapse
Affiliation(s)
- Tingting Li
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Dongxia Liu
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yadi Yang
- Institute of Immunology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Jiali Guo
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Yujie Feng
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Xinmo Zhang
- The Second Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Shilong Cheng
- The First Clinical Medical School, Lanzhou University, Lanzhou, 730000, China
| | - Jie Feng
- Institute of Pathology, School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China.
| |
Collapse
|
14
|
Chan KK, Tan TJC, Narayanan KK, Procko E. An engineered decoy receptor for SARS-CoV-2 broadly binds protein S sequence variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.10.18.344622. [PMID: 33398275 PMCID: PMC7781310 DOI: 10.1101/2020.10.18.344622] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The spike S of SARS-CoV-2 recognizes ACE2 on the host cell membrane to initiate entry. Soluble decoy receptors, in which the ACE2 ectodomain is engineered to block S with high affinity, potently neutralize infection and, due to close similarity with the natural receptor, hold out the promise of being broadly active against virus variants without opportunity for escape. Here, we directly test this hypothesis. We find an engineered decoy receptor, sACE2 2 .v2.4, tightly binds S of SARS-associated viruses from humans and bats, despite the ACE2-binding surface being a region of high diversity. Saturation mutagenesis of the receptor-binding domain (RBD) followed by in vitro selection, with wild type ACE2 and the engineered decoy competing for binding sites, failed to find S mutants that discriminate in favor of the wild type receptor. Variant N501Y in the RBD, which has emerged in a rapidly spreading lineage (B.1.1.7) in England, enhances affinity for wild type ACE2 20-fold but remains tightly bound to engineered sACE22.v2.4. We conclude that resistance to engineered decoys will be rare and that decoys may be active against future outbreaks of SARS-associated betacoronaviruses.
Collapse
Affiliation(s)
- Kui K Chan
- Orthogonal Biologics, Champaign IL 61821
| | - Timothy J C Tan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Krishna K Narayanan
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| | - Erik Procko
- Department of Biochemistry and Cancer Center at Illinois, University of Illinois, Urbana IL 61801
| |
Collapse
|
15
|
Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141364. [PMID: 32836117 PMCID: PMC7836549 DOI: 10.1016/j.scitotenv.2020.141364] [Citation(s) in RCA: 263] [Impact Index Per Article: 52.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 04/14/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
Collapse
Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| |
Collapse
|
16
|
Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 749:141364. [PMID: 32836117 DOI: 10.20944/preprints202007.0471.v1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 07/27/2020] [Accepted: 07/28/2020] [Indexed: 05/18/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
Collapse
Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| |
Collapse
|
17
|
Jones DL, Baluja MQ, Graham DW, Corbishley A, McDonald JE, Malham SK, Hillary LS, Connor TR, Gaze WH, Moura IB, Wilcox MH, Farkas K. Shedding of SARS-CoV-2 in feces and urine and its potential role in person-to-person transmission and the environment-based spread of COVID-19. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020. [PMID: 32836117 DOI: 10.1016/j.scitotenv.2020.141364pmid-32836117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The recent detection of SARS-CoV-2 RNA in feces has led to speculation that it can be transmitted via the fecal-oral/ocular route. This review aims to critically evaluate the incidence of gastrointestinal (GI) symptoms, the quantity and infectivity of SARS-CoV-2 in feces and urine, and whether these pose an infection risk in sanitary settings, sewage networks, wastewater treatment plants, and the wider environment (e.g. rivers, lakes and marine waters). A review of 48 independent studies revealed that severe GI dysfunction is only evident in a small number of COVID-19 cases, with 11 ± 2% exhibiting diarrhea and 12 ± 3% exhibiting vomiting and nausea. In addition to these cases, SARS-CoV-2 RNA can be detected in feces from some asymptomatic, mildly- and pre-symptomatic individuals. Fecal shedding of the virus peaks in the symptomatic period and can persist for several weeks, but with declining abundances in the post-symptomatic phase. SARS-CoV-2 RNA is occasionally detected in urine, but reports in fecal samples are more frequent. The abundance of the virus genetic material in both urine (ca. 102-105 gc/ml) and feces (ca. 102-107 gc/ml) is much lower than in nasopharyngeal fluids (ca. 105-1011 gc/ml). There is strong evidence of multiplication of SARS-CoV-2 in the gut and infectious virus has occasionally been recovered from both urine and stool samples. The level and infectious capability of SARS-CoV-2 in vomit remain unknown. In comparison to enteric viruses transmitted via the fecal-oral route (e.g. norovirus, adenovirus), the likelihood of SARS-CoV-2 being transmitted via feces or urine appears much lower due to the lower relative amounts of virus present in feces/urine. The biggest risk of transmission will occur in clinical and care home settings where secondary handling of people and urine/fecal matter occurs. In addition, while SARS-CoV-2 RNA genetic material can be detected by in wastewater, this signal is greatly reduced by conventional treatment. Our analysis also suggests the likelihood of infection due to contact with sewage-contaminated water (e.g. swimming, surfing, angling) or food (e.g. salads, shellfish) is extremely low or negligible based on very low predicted abundances and limited environmental survival of SARS-CoV-2. These conclusions are corroborated by the fact that tens of million cases of COVID-19 have occurred globally, but exposure to feces or wastewater has never been implicated as a transmission vector.
Collapse
Affiliation(s)
- David L Jones
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia.
| | | | - David W Graham
- School of Engineering, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Alexander Corbishley
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, Easter Bush Campus Midlothian, EH25 9RG, UK
| | - James E McDonald
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Shelagh K Malham
- School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| | - Luke S Hillary
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Thomas R Connor
- Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Public Health Wales, University Hospital of Wales, Cardiff CF14 4XW, UK
| | - William H Gaze
- European Centre for Environment and Human Health, University of Exeter Medical School, ESI, Penryn Campus, TR10 9FE, UK
| | - Ines B Moura
- Leeds Institute for Medical Research, Faculty of Medicine and Health, University of Leeds, Leeds LS1 3EX, UK
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - Kata Farkas
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor, Gwynedd LL57 2UW, UK; School of Ocean Sciences, Bangor University, Menai Bridge, Anglesey LL59 5AB, UK
| |
Collapse
|
18
|
Haider N, Rothman-Ostrow P, Osman AY, Arruda LB, Macfarlane-Berry L, Elton L, Thomason MJ, Yeboah-Manu D, Ansumana R, Kapata N, Mboera L, Rushton J, McHugh TD, Heymann DL, Zumla A, Kock RA. COVID-19-Zoonosis or Emerging Infectious Disease? Front Public Health 2020; 8:596944. [PMID: 33324602 PMCID: PMC7725765 DOI: 10.3389/fpubh.2020.596944] [Citation(s) in RCA: 73] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/20/2020] [Indexed: 12/20/2022] Open
Abstract
The World Health Organization defines a zoonosis as any infection naturally transmissible from vertebrate animals to humans. The pandemic of Coronavirus disease (COVID-19) caused by SARS-CoV-2 has been classified as a zoonotic disease, however, no animal reservoir has yet been found, so this classification is premature. We propose that COVID-19 should instead be classified an "emerging infectious disease (EID) of probable animal origin." To explore if COVID-19 infection fits our proposed re-categorization vs. the contemporary definitions of zoonoses, we reviewed current evidence of infection origin and transmission routes of SARS-CoV-2 virus and described this in the context of known zoonoses, EIDs and "spill-over" events. Although the initial one hundred COVID-19 patients were presumably exposed to the virus at a seafood Market in China, and despite the fact that 33 of 585 swab samples collected from surfaces and cages in the market tested positive for SARS-CoV-2, no virus was isolated directly from animals and no animal reservoir was detected. Elsewhere, SARS-CoV-2 has been detected in animals including domesticated cats, dogs, and ferrets, as well as captive-managed mink, lions, tigers, deer, and mice confirming zooanthroponosis. Other than circumstantial evidence of zoonotic cases in mink farms in the Netherlands, no cases of natural transmission from wild or domesticated animals have been confirmed. More than 40 million human COVID-19 infections reported appear to be exclusively through human-human transmission. SARS-CoV-2 virus and COVID-19 do not meet the WHO definition of zoonoses. We suggest SARS-CoV-2 should be re-classified as an EID of probable animal origin.
Collapse
Affiliation(s)
- Najmul Haider
- The Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| | - Peregrine Rothman-Ostrow
- Department of Epidemiology and Population Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | | | - Liã Bárbara Arruda
- Division of Infection and Immunity, Department of Infection, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Laura Macfarlane-Berry
- Epidemiology and One Health, Animal Health Policy Branch, Department of Agriculture, Water and the Environment, Canberra, ACT, Australia
| | - Linzy Elton
- Division of Infection and Immunity, Department of Infection, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Margaret J. Thomason
- Division of Infection and Immunity, Department of Infection, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - Dorothy Yeboah-Manu
- Bacteriology Department, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Rashid Ansumana
- Department of Community Medicine, Njala University, Bo, Sierra Leone
| | - Nathan Kapata
- Zambia National Public Health Institute, Ministry of Health, Lusaka, Zambia
| | - Leonard Mboera
- South African Centre for Infectious Diseases Surveillance (SACIDS) Foundation for One Health, Sokoine University of Agriculture, Morogoro, Tanzania
| | - Jonathan Rushton
- Department of Epidemiology and Population Health, Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Timothy D. McHugh
- Division of Infection and Immunity, Department of Infection, Centre for Clinical Microbiology, University College London, London, United Kingdom
| | - David L. Heymann
- Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Alimuddin Zumla
- Division of Infection and Immunity, Department of Infection, Centre for Clinical Microbiology, University College London, London, United Kingdom
- National Institute of Health Research, Biomedical Research Centre, University College London Hospitals, National Health Service Foundation Trust, London, United Kingdom
| | - Richard A. Kock
- The Royal Veterinary College, University of London, Hertfordshire, United Kingdom
| |
Collapse
|
19
|
Hassan SS, Choudhury PP, Uversky VN, Dayhoff GW, Aljabali AAA, Uhal BD, Lundstrom K, Rezaei N, Seyran M, Pizzol D, Adadi P, Lal A, Soares A, Abd El-aziz TM, Kandimalla R, Tambuwala M, Azad GK, Sherchan SP, Baetas-da-cruz W, Takayama K, Serrano-aroca Á, Chauhan G, Palu G, Brufsky AM. Variability of Accessory Proteins Rules the SARS-CoV-2 Pathogenicity.. [DOI: 10.1101/2020.11.06.372227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
Abstract
AbstractThe coronavirus disease 2019 (COVID-19) is caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which is pandemic with an estimated fatality rate less than 1% is ongoing. SARS-CoV-2 accessory proteins ORF3a, ORF6, ORF7a, ORF7b, ORF8, and ORF10 with putative functions to manipulate host immune mechanisms such as interferons, immune signaling receptor NLRP3 (NOD-, LRR-, and pyrin domain-containing 3) inflammasome, inflammatory cytokines such as interleukin 1β(IL-1β) are critical in COVID-19 pathology. Outspread variations of each of the six accessory proteins of all complete proteomes (available as of October 26, 2020, in the National Center for Biotechnology Information depository) of SARS-CoV-2, were observed across six continents. Across all continents, the decreasing order of percentage of unique variations in the accessory proteins was found to be ORF3a>ORF8>ORF7a>ORF6>ORF10>ORF7b. The highest and lowest unique variations of ORF3a were observed in South America and Oceania, respectively. This finding suggests that the wide variations of accessory proteins seem to govern the pathogenicity of SARS-CoV-2, and consequently, certain propositions and recommendations can be made in the public interest.
Collapse
|
20
|
Johansen MD, Irving A, Montagutelli X, Tate MD, Rudloff I, Nold MF, Hansbro NG, Kim RY, Donovan C, Liu G, Faiz A, Short KR, Lyons JG, McCaughan GW, Gorrell MD, Cole A, Moreno C, Couteur D, Hesselson D, Triccas J, Neely GG, Gamble JR, Simpson SJ, Saunders BM, Oliver BG, Britton WJ, Wark PA, Nold-Petry CA, Hansbro PM. Animal and translational models of SARS-CoV-2 infection and COVID-19. Mucosal Immunol 2020; 13:877-891. [PMID: 32820248 PMCID: PMC7439637 DOI: 10.1038/s41385-020-00340-z] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/30/2020] [Accepted: 07/31/2020] [Indexed: 02/06/2023]
Abstract
COVID-19 is causing a major once-in-a-century global pandemic. The scientific and clinical community is in a race to define and develop effective preventions and treatments. The major features of disease are described but clinical trials have been hampered by competing interests, small scale, lack of defined patient cohorts and defined readouts. What is needed now is head-to-head comparison of existing drugs, testing of safety including in the background of predisposing chronic diseases, and the development of new and targeted preventions and treatments. This is most efficiently achieved using representative animal models of primary infection including in the background of chronic disease with validation of findings in primary human cells and tissues. We explore and discuss the diverse animal, cell and tissue models that are being used and developed and collectively recapitulate many critical aspects of disease manifestation in humans to develop and test new preventions and treatments.
Collapse
Affiliation(s)
- M D Johansen
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - A Irving
- Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, ZJU International Campus, Haining, China
- Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - X Montagutelli
- Department of Genomes and Genetics, Institut Pasteur, Paris, France
| | - M D Tate
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, VIC, Australia
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
| | - I Rudloff
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Department of Paediatrics, Monash University, Clayton, VIC, 3168, Australia
| | - M F Nold
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
- Monash Newborn, Monash Children's Hospital, Clayton, VIC, Australia
| | - N G Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - R Y Kim
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - C Donovan
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - G Liu
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - A Faiz
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - K R Short
- School of Chemistry and Molecular Biosciences and Australian Infectious Diseases Research Centre, The University of Queensland, Brisbane, Australia
| | - J G Lyons
- Centenary Institute and Dermatology, The University of Sydney and Cancer Services, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - G W McCaughan
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - M D Gorrell
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - A Cole
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - C Moreno
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - D Couteur
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, and Faculty of Medicine and Health, Concord Clinical School, ANZAC Research Institute and Centre for Education and Research on Ageing, Sydney, Australia
| | - D Hesselson
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - J Triccas
- Discipline of Infectious Diseases and Immunology, Central Clinical School, Faculty of Medicine and Health and the Charles Perkins Centre, The University of Sydney, Camperdown, Sydney, Australia
| | - G G Neely
- Dr. John and Anne Chong Lab for Functional Genomics, Charles Perkins Centre, Centenary Institute, and School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - J R Gamble
- Centenary Institute and Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - S J Simpson
- Charles Perkins Centre and School of Life and Environmental Sciences, University of Sydney, and Faculty of Medicine and Health, Concord Clinical School, ANZAC Research Institute and Centre for Education and Research on Ageing, Sydney, Australia
| | - B M Saunders
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
| | - B G Oliver
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia
- Woolcock Institute of Medical Research, Sydney, Australia
| | - W J Britton
- Centenary Institute, The University of Sydney and Department of Clinical Immunology, Royal Prince Alfred Hospital, Sydney, NSW, Australia
| | - P A Wark
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia
| | - C A Nold-Petry
- Department of Molecular and Translational Sciences, Monash University, Clayton, VIC, Australia
- Ritchie Centre, Hudson Institute of Medical Research, Clayton, VIC, 3168, Australia
| | - P M Hansbro
- Centre for Inflammation, Centenary Institute and University of Technology Sydney, Faculty of Science, Sydney, Australia.
- Priority Research Centre for Healthy Lungs, Hunter Medical Research Institute and University of Newcastle, Newcastle, NSW, Australia.
| |
Collapse
|
21
|
Elie B, Alizon S. Analyses génomiques et phylodynamiques du Sars-CoV-2. REVUE FRANCOPHONE DES LABORATOIRES 2020; 2020:57-62. [PMID: 33163105 PMCID: PMC7604060 DOI: 10.1016/s1773-035x(20)30314-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Dans la lignée des épidémies récentes des virus Ebola et Zika, la pandémie de Covid-19 a donné lieu à une avalanche de données génomiques. Celles-ci ont permis de mieux comprendre l’origine de ce virus, de dater son apparition en Chine mais aussi en France et d’analyser la propagation de l’épidémie grâce aux techniques issues du champ émergent qu’est la phylodynamique.
Collapse
Affiliation(s)
- Baptiste Elie
- Laboratoire maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (UMR CNRS 5290, IRD, UM), 911 avenue Agropolis, 34394 Montpellier cedex 5, France
- École normale supérieure Paris-Saclay, Université Paris-Saclay, 61 Avenue du Président-Wilson, 94230 Cachan, France
| | - Samuel Alizon
- Laboratoire maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (UMR CNRS 5290, IRD, UM), 911 avenue Agropolis, 34394 Montpellier cedex 5, France
| |
Collapse
|
22
|
Shen M, Liu C, Xu R, Ruan Z, Zhao S, Zhang H, Wang W, Huang X, Yang L, Tang Y, Yang T, Jia X. Predicting the Animal Susceptibility and Therapeutic Drugs to SARS-CoV-2 Based on Spike Glycoprotein Combined With ACE2. Front Genet 2020; 11:575012. [PMID: 33193684 PMCID: PMC7645152 DOI: 10.3389/fgene.2020.575012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 09/30/2020] [Indexed: 12/29/2022] Open
Abstract
Recently, a few animals have been frequently reported to have been diagnosed with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Whether they are SARS-CoV-2 intermediate hosts is worthy of great attention. The interaction of SARS-CoV-2 spike protein and its acceptor protein ACE2 is an important issue in determining viral host range and cross-species infection, while the binding capacity of Spike protein to ACE2 of different species is unknown. Here, we used the atomic structure model of SARS-CoV-2 and human ACE2 to assess the receptor utilization capacity of ACE2s from 10 kinds of animals. Results show that chimpanzees, domestic cats and cattles are more susceptible to infection by SARS-CoV-2. Cats in particular, such as pet cats and stray cats, interact very closely with humans, implying the necessity to carefully evaluate the risk of cats during the current COVID-19 pandemic. Furthermore, based on ACE2(cats)-SARS-CoV-2-RBD model, through high-throughput screening methods using a pool of 30,000 small molecules, eight compounds were selected for binding free energy calculations. All the eight compounds can effectively interfere with the binding of ACE2 and Spike protein, especially Nelfinavir, providing drug candidates for the treatment and prevention of SARS-CoV-2, suggesting further assessment of the anti-SARS-CoV-2 activity of these compounds in cell culture. Although we only reported the results of the simulation, and more laboratory and epidemiological investigation are required. Like cats are a risk factor, we can further detect SARS-CoV-2 according to the susceptibility of different animals, find the potential host of infection, and completely cut off the living space of the virus. Especially, cats could be a choice of animal model for screening antiviral drugs or vaccine candidates against SARS-CoV-2.
Collapse
Affiliation(s)
- Min Shen
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Chao Liu
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Run Xu
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Zijing Ruan
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Shiying Zhao
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Huidong Zhang
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Wen Wang
- West China School of Public Health, Sichuan University, Chengdu, China
| | - Xinhe Huang
- School of Life Sciences and Engineering, Southwest Jiaotong University, Chengdu, China
| | - Li Yang
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Yong Tang
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| | - Tai Yang
- School of Pharmacy, Chengdu Medical College, Chengdu, China
| | - Xu Jia
- Non-coding RNA and Drug Discovery Key Laboratory of Sichuan Province, Chengdu Medical College, Chengdu, China
| |
Collapse
|
23
|
Tomaszewski T, DeVries RS, Dong M, Bhatia G, Norsworthy MD, Zheng X, Caetano-Anollés G. New Pathways of Mutational Change in SARS-CoV-2 Proteomes Involve Regions of Intrinsic Disorder Important for Virus Replication and Release. Evol Bioinform Online 2020; 16:1176934320965149. [PMID: 33149541 PMCID: PMC7586267 DOI: 10.1177/1176934320965149] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 09/16/2020] [Indexed: 12/21/2022] Open
Abstract
The massive worldwide spread of the SARS-CoV-2 virus is fueling the COVID-19 pandemic. Since the first whole-genome sequence was published in January 2020, a growing database of tens of thousands of viral genomes has been constructed. This offers opportunities to study pathways of molecular change in the expanding viral population that can help identify molecular culprits of virulence and virus spread. Here we investigate the genomic accumulation of mutations at various time points of the early pandemic to identify changes in mutationally highly active genomic regions that are occurring worldwide. We used the Wuhan NC_045512.2 sequence as a reference and sampled 15 342 indexed sequences from GISAID, translating them into proteins and grouping them by month of deposition. The per-position amino acid frequencies and Shannon entropies of the coding sequences were calculated for each month, and a map of intrinsic disorder regions and binding sites was generated. The analysis revealed dominant variants, most of which were located in loop regions and on the surface of the proteins. Mutation entropy decreased between March and April of 2020 after steady increases at several sites, including the D614G mutation site of the spike (S) protein that was previously found associated with higher case fatality rates and at sites of the NSP12 polymerase and the NSP13 helicase proteins. Notable expanding mutations include R203K and G204R of the nucleocapsid (N) protein inter-domain linker region and G251V of the viroporin encoded by ORF3a between March and April. The regions spanning these mutations exhibited significant intrinsic disorder, which was enhanced and decreased by the N-protein and viroporin 3a protein mutations, respectively. These results predict an ongoing mutational shift from the spike and replication complex to other regions, especially to encoded molecules known to represent major β-interferon antagonists. The study provides valuable information for therapeutics and vaccine design, as well as insight into mutation tendencies that could facilitate preventive control.
Collapse
Affiliation(s)
- Tre Tomaszewski
- Department of Information Sciences, University of Illinois, Urbana, IL, USA
| | - Ryan S DeVries
- Department of Information Sciences, University of Illinois, Urbana, IL, USA
| | - Mengyi Dong
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL, USA
| | - Gitanshu Bhatia
- Department of Agricultural & Biological Engineering, University of Illinois, Urbana, IL, USA
| | | | - Xuying Zheng
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | | |
Collapse
|
24
|
Abraham P, Cherian S, Potdar V. Genetic characterization of SARS-CoV-2 & implications for epidemiology, diagnostics & vaccines in India. Indian J Med Res 2020; 152:12-15. [PMID: 32896836 PMCID: PMC7853292 DOI: 10.4103/ijmr.ijmr_3667_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Indexed: 01/01/2023] Open
Affiliation(s)
- Priya Abraham
- ICMR-National Institute of Virology, Pune 411 001, Maharashtra, India
| | - Sarah Cherian
- Bioinformatics & Data management Group, Pune 411 001, Maharashtra, India
| | - Varsha Potdar
- Human Influenza Group, Pune 411 001, Maharashtra, India
| |
Collapse
|
25
|
Schreiber G. The Role of Type I Interferons in the Pathogenesis and Treatment of COVID-19. Front Immunol 2020; 11:595739. [PMID: 33117408 PMCID: PMC7561359 DOI: 10.3389/fimmu.2020.595739] [Citation(s) in RCA: 80] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/16/2020] [Indexed: 12/16/2022] Open
Abstract
Type I interferons (IFN-I) were first discovered over 60 years ago in a classical experiment by Isaacs and Lindenman, who showed that IFN-Is possess antiviral activity. Later, it became one of the first approved protein drugs using heterologous protein expression systems, which allowed its large-scale production. It has been approved, and widely used in a pleiotropy of diseases, including multiple-sclerosis, hepatitis B and C, and some forms of cancer. Preliminary clinical data has supported its effectiveness against potential pandemic pathogens such as Ebola and SARS. Still, more efficient and specific drugs have taken its place in treating such diseases. The COVID-19 global pandemic has again lifted the status of IFN-Is to become one of the more promising drug candidates, with initial clinical trials showing promising results in reducing the severity and duration of the disease. Although SARS-CoV-2 inhibits the production of IFNβ and thus obstructs the innate immune response to this virus, it is sensitive to the antiviral activity of externally administrated IFN-Is. In this review I discuss the diverse modes of biological actions of IFN-Is and how these are related to biophysical parameters of IFN-I-receptor interaction and cell-type specificity in light of the large variety of binding affinities of the different IFN-I subtypes towards the common interferon receptor. Furthermore, I discuss how these may guide the optimized use IFN-Is in combatting COVID-19.
Collapse
Affiliation(s)
- Gideon Schreiber
- Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel
| |
Collapse
|
26
|
Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
Collapse
Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
| |
Collapse
|
27
|
Ladner JT, Larsen BB, Bowers JR, Hepp CM, Bolyen E, Folkerts M, Sheridan K, Pfeiffer A, Yaglom H, Lemmer D, Sahl JW, Kaelin EA, Maqsood R, Bokulich NA, Quirk G, Watts TD, Komatsu KK, Waddell V, Lim ES, Caporaso JG, Engelthaler DM, Worobey M, Keim P. An Early Pandemic Analysis of SARS-CoV-2 Population Structure and Dynamics in Arizona. mBio 2020; 11:e02107-20. [PMID: 32887735 PMCID: PMC7474171 DOI: 10.1128/mbio.02107-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
In December of 2019, a novel coronavirus, SARS-CoV-2, emerged in the city of Wuhan, China, causing severe morbidity and mortality. Since then, the virus has swept across the globe, causing millions of confirmed infections and hundreds of thousands of deaths. To better understand the nature of the pandemic and the introduction and spread of the virus in Arizona, we sequenced viral genomes from clinical samples tested at the TGen North Clinical Laboratory, the Arizona Department of Health Services, and those collected as part of community surveillance projects at Arizona State University and the University of Arizona. Phylogenetic analysis of 84 genomes from across Arizona revealed a minimum of 11 distinct introductions inferred to have occurred during February and March. We show that >80% of our sequences descend from strains that were initially circulating widely in Europe but have since dominated the outbreak in the United States. In addition, we show that the first reported case of community transmission in Arizona descended from the Washington state outbreak that was discovered in late February. Notably, none of the observed transmission clusters are epidemiologically linked to the original travel-related case in the state, suggesting successful early isolation and quarantine. Finally, we use molecular clock analyses to demonstrate a lack of identifiable, widespread cryptic transmission in Arizona prior to the middle of February 2020.IMPORTANCE As the COVID-19 pandemic swept across the United States, there was great differential impact on local and regional communities. One of the earliest and hardest hit regions was in New York, while at the same time Arizona (for example) had low incidence. That situation has changed dramatically, with Arizona now having the highest rate of disease increase in the country. Understanding the roots of the pandemic during the initial months is essential as the pandemic continues and reaches new heights. Genomic analysis and phylogenetic modeling of SARS-COV-2 in Arizona can help to reconstruct population composition and predict the earliest undetected introductions. This foundational work represents the basis for future analysis and understanding as the pandemic continues.
Collapse
Affiliation(s)
- Jason T Ladner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Brendan B Larsen
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Jolene R Bowers
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Crystal M Hepp
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, Arizona, USA
| | - Evan Bolyen
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Megan Folkerts
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Krystal Sheridan
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Ashlyn Pfeiffer
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Hayley Yaglom
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Darrin Lemmer
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Jason W Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
| | - Emily A Kaelin
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - Rabia Maqsood
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - Nicholas A Bokulich
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - Grace Quirk
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Thomas D Watts
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | | | - Victor Waddell
- Bureau of Laboratory Services, Arizona Department of Health Services, Phoenix, Arizona, USA
| | - Efrem S Lim
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
- Center for Fundamental and Applied Microbiomics, Biodesign Institute, Tempe, Arizona, USA
| | - J Gregory Caporaso
- Center for Applied Microbiome Science, Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| | - David M Engelthaler
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, Arizona, USA
- Pathogen and Microbiome Division, Translational Genomics Research Institute, Flagstaff, Arizona, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA
| |
Collapse
|
28
|
Hoque MN, Chaudhury A, Akanda MAM, Hossain MA, Islam MT. Genomic diversity and evolution, diagnosis, prevention, and therapeutics of the pandemic COVID-19 disease. PeerJ 2020; 8:e9689. [PMID: 33005486 PMCID: PMC7510477 DOI: 10.7717/peerj.9689] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
The coronavirus disease 19 (COVID-19) is a highly transmittable and pathogenic viral infection caused by a novel evolutionarily divergent RNA virus, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The virus first emerged in Wuhan, China in December 2019, and subsequently spreaded around the world. Genomic analyses revealed that this zoonotic virus may be evolved naturally but not a purposefully manipulated laboratory construct. However, currently available data are not sufficient to precisely conclude the origin of this fearsome virus. Comprehensive annotations of the whole-genomes revealed hundreds of nucleotides, and amino acids mutations, substitutions and/or deletions at different positions of the ever changing SARS-CoV-2 genome. The spike (S) glycoprotein of SARS-CoV-2 possesses a functional polybasic (furin) cleavage site at the S1-S2 boundary through the insertion of 12 nucleotides. It leads to the predicted acquisition of 3-O-linked glycan around the cleavage site. Although real-time RT-PCR methods targeting specific gene(s) have widely been used to diagnose the COVID-19 patients, however, recently developed more convenient, cheap, rapid, and specific diagnostic tools targeting antigens or CRISPR-Cas-mediated method or a newly developed plug and play method should be available for the resource-poor developing countries. A large number of candidate drugs, vaccines and therapies have shown great promise in early trials, however, these candidates of preventive or therapeutic agents have to pass a long path of trials before being released for the practical application against COVID-19. This review updates current knowledge on origin, genomic evolution, development of the diagnostic tools, and the preventive or therapeutic remedies of the COVID-19. We also discussed the future scopes for research, effective management, and surveillance of the newly emerged COVID-19 disease.
Collapse
Affiliation(s)
- M. Nazmul Hoque
- Department of Gynecology, Obstetrics and Reproductive Health, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md Abdul Mannan Akanda
- Department of Plant Pathology, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| | - M. Anwar Hossain
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
- Jashore University of Science and Technology, Jashore, Bangladesh
| | - Md Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Gazipur, Bangladesh
| |
Collapse
|
29
|
Domańska-Blicharz K, Woźniakowski G, Konopka B, Niemczuk K, Welz M, Rola J, Socha W, Orłowska A, Antas M, Śmietanka K, Cuvelier-Mizak B. Animal Coronaviruses in the Light of COVID-19. J Vet Res 2020; 64:333-345. [PMID: 32984621 PMCID: PMC7497757 DOI: 10.2478/jvetres-2020-0050] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/20/2020] [Indexed: 12/24/2022] Open
Abstract
Coronaviruses are extremely susceptible to genetic changes due to the characteristic features of the genome structure, life cycle and environmental pressure. Their remarkable variability means that they can infect many different species of animals and cause different disease symptoms. Moreover, in some situations, coronaviruses might be transmitted across species. Although they are commonly found in farm, companion and wild animals, causing clinical and sometimes serious signs resulting in significant economic losses, not all of them have been classified by the World Organization for Animal Health (OIE) as hazardous and included on the list of notifiable diseases. Currently, only three diseases caused by coronaviruses are on the OIE list of notifiable terrestrial and aquatic animal diseases. However, none of these three entails any administrative measures. The emergence of the SARS-CoV-2 infections that have caused the COVID-19 pandemic in humans has proved that the occurrence and variability of coronaviruses is highly underestimated in the animal reservoir and reminded us of the critical importance of the One Health approach. Therefore, domestic and wild animals should be intensively monitored, both to broaden our knowledge of the viruses circulating among them and to understand the mechanisms of the emergence of viruses of relevance to animal and human health.
Collapse
Affiliation(s)
| | - Grzegorz Woźniakowski
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | | | - Krzysztof Niemczuk
- Director General, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Mirosław Welz
- General Veterinary Inspectorate, 00-930Warsaw, Poland
| | - Jerzy Rola
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Wojciech Socha
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Anna Orłowska
- Department of Virology, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Marta Antas
- Department of Swine Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Krzysztof Śmietanka
- Department of Poultry Diseases, National Veterinary Research Institute, 24-100Puławy, Poland
| | - Beata Cuvelier-Mizak
- Department of Veterinary Pharmacy, National Veterinary Research Institute, 24-100Puławy, Poland
| |
Collapse
|
30
|
Jenkins MM, McCaw TR, Goepfert PA. Mechanistic inferences from clinical reports of SARS-CoV-2. Infect Dis (Lond) 2020; 52:527-537. [PMID: 32459123 PMCID: PMC7265107 DOI: 10.1080/23744235.2020.1769853] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 01/08/2023] Open
Abstract
SARS-CoV-2 was identified as the causative pathogen in an outbreak of viral pneumonia cases originating in Wuhan, China, with an ensuing rapid global spread that led it to be declared a pandemic by the WHO on March 11, 2020. Given the threat to public health posed by sequelae of SARS-CoV-2 infection, the literature surrounding patient presentation in severe and non-severe cases, transmission rates and routes, management strategies, and initial clinical trial results have become available at an unprecedented pace. In this review we collate current clinical and immunologic reports, comparing these to reports of previous coronaviruses to identify mechanisms driving progression to severe disease in some patients. In brief, we propose a model wherein dysregulated type I interferon signalling leads to aberrant recruitment and accumulation of innate immune lineages in the lung, impairing establishment of productive adaptive responses, and permitting a pathologic pro-inflammatory state. Finally, we extend these findings to suggest possible treatment options that may merit investigation in randomized clinical trials.
Collapse
Affiliation(s)
- Meagan M. Jenkins
- Department of Medicine, Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Tyler R. McCaw
- Department of Medicine, Division of Clinical Immunology & Rheumatology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Paul A. Goepfert
- Department of Medicine, Division of Infectious Diseases, University of Alabama at Birmingham, Birmingham, AL, USA
| |
Collapse
|
31
|
Jawaid Akhtar M. COVID19 inhibitors: A prospective therapeutics. Bioorg Chem 2020; 101:104027. [PMID: 32629280 PMCID: PMC7297670 DOI: 10.1016/j.bioorg.2020.104027] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 06/12/2020] [Accepted: 06/14/2020] [Indexed: 12/14/2022]
Abstract
The inhibition of viral targets might provide new therapies for coronavirus disease abbreviated as COVID-19. The rational drug design identified as much of the recent discoveries of potent drugs molecule against any targets. This results in an improvement in bindings for better potency and selectivity. The drugs containing ethanolamine/propylamine fragments along with heterocycles have shown potential antiviral results. Similarly, there is the possibility of controlling the COVID-19 infection by nucleotide analogues. Here we also highlight drugs ACEIs/ARBs inhibitory discussing both their advantages and disadvantages. The class of compounds/antibodies inhibiting interleukin-6 works in antirheumatoid drugs are found useful in alleviating overactive inflammatory responses in the lungs of the patient. These inclusion based approaches counter some of the side-effects associated with the heterocycles and also potentiate the efficacy of the molecules. In this review article, design strategies for some of the drugs effective against SARS-CoV-2 are represented. The review also focuses on the listing of drugs that are currently testing under clinical trials for the COVID-19 virus with their mechanism of action. This conversation undertakes the opportunity to do a bit for the newer researchers working in this arena.
Collapse
Affiliation(s)
- Md Jawaid Akhtar
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Ghal Kalan, Ferozpur G.T. Road, Moga 142001, Punjab, India.
| |
Collapse
|
32
|
A palindromic RNA sequence as a common breakpoint contributor to copy-choice recombination in SARS-COV-2. Arch Virol 2020; 165:2341-2348. [PMID: 32737584 PMCID: PMC7394270 DOI: 10.1007/s00705-020-04750-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 07/20/2020] [Indexed: 01/05/2023]
Abstract
Much remains unknown concerning the origin of the novel pandemic coronavirus that has raged across the globe since emerging in Wuhan of Hubei province, near the center of the People’s Republic of China, in December of 2019. All current members of the family Coronaviridae have arisen by a combination of incremental adaptive mutations, against the backdrop of many recombinational events throughout the past, rendering each a unique mosaic of RNA sequences from diverse sources. The consensus among virologists is that the base sequence of the novel coronavirus, designated SARS-CoV-2, was derived from a common ancestor of a bat coronavirus, represented by the strain RaTG13, isolated in Yunnan province in 2013. Into that ancestral genetic background, several recombination events have since occurred from other divergent bat-derived coronaviruses, resulting in localized discordance between the two. One such event left SARS-CoV-2 with a receptor binding domain (RBD) capable of binding the human ACE-2 receptor lacking in RaTG13, and a second event uniquely added to SARS-CoV-2 a site specific for furin, capable of efficient endoproteolytic cleavage and activation of the spike glycoprotein responsible for virus entry and cell fusion. This paper demonstrates by bioinformatic analysis that such recombinational events are facilitated by short oligonucleotide “breakpoint sequences”, similar to CAGAC, that direct recombination naturally to certain positions in the genome at the boundaries between blocks of RNA code and potentially RNA structure. This “breakpoint sequence hypothesis” provides a natural explanation for the biogenesis of SARS-CoV-2 over time and in the wild.
Collapse
|
33
|
MacLean OA, Lytras S, Weaver S, Singer JB, Boni MF, Lemey P, Kosakovsky Pond SL, Robertson DL. Natural selection in the evolution of SARS-CoV-2 in bats, not humans, created a highly capable human pathogen. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020. [PMID: 32577659 DOI: 10.1101/2020.05.28.122366] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
RNA viruses are proficient at switching host species, and evolving adaptations to exploit the new host's cells efficiently. Surprisingly, SARS-CoV-2 has apparently required no significant adaptation to humans since the start of the COVID-19 pandemic, with no observed selective sweeps since genome sampling began. Here we assess the types of natural selection taking place in Sarbecoviruses in horseshoe bats versus SARS-CoV-2 evolution in humans. While there is moderate evidence of diversifying positive selection in SARS-CoV-2 in humans, it is limited to the early phase of the pandemic, and purifying selection is much weaker in SARS-CoV-2 than in related bat Sarbecoviruses . In contrast, our analysis detects significant positive episodic diversifying selection acting on the bat virus lineage SARS-CoV-2 emerged from, accompanied by an adaptive depletion in CpG composition presumed to be linked to the action of antiviral mechanisms in ancestral hosts. The closest bat virus to SARS-CoV-2, RmYN02 (sharing an ancestor ∼1976), is a recombinant with a structure that includes differential CpG content in Spike; clear evidence of coinfection and evolution in bats without involvement of other species. Collectively our results demonstrate the progenitor of SARS-CoV-2 was capable of near immediate human-human transmission as a consequence of its adaptive evolutionary history in bats, not humans.
Collapse
|
34
|
Parlikar A, Kalia K, Sinha S, Patnaik S, Sharma N, Vemuri SG, Sharma G. Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2. PeerJ 2020; 8:e9576. [PMID: 32742815 PMCID: PMC7370936 DOI: 10.7717/peerj.9576] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 06/29/2020] [Indexed: 01/10/2023] Open
Abstract
Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.
Collapse
Affiliation(s)
- Arohi Parlikar
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Kishan Kalia
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Shruti Sinha
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Sucheta Patnaik
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Neeraj Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Sai Gayatri Vemuri
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| | - Gaurav Sharma
- Institute of Bioinformatics and Applied Biotechnology (IBAB), Bengaluru, Karnataka, India
| |
Collapse
|
35
|
Abdel-Moneim AS, Abdelwhab EM. Evidence for SARS-CoV-2 Infection of Animal Hosts. Pathogens 2020; 9:E529. [PMID: 32629960 PMCID: PMC7400078 DOI: 10.3390/pathogens9070529] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/27/2020] [Accepted: 06/28/2020] [Indexed: 12/23/2022] Open
Abstract
COVID-19 is the first known pandemic caused by a coronavirus, SARS-CoV-2, which is the third virus in the family Coronaviridae to cause fatal infections in humans after SARS-CoV and MERS-CoV. Animals are involved in the COVID-19 pandemic. This review summarizes the role of animals as reservoirs, natural hosts and experimental models. SARS-CoV-2 originated from animal reservoir, most likely bats and/or pangolins. Anthroponotic transmission has been reported in cats, dogs, tigers, lions and minks. As of now, there is no a strong evidence for natural animal-to-human transmission or sustained animal-to-animal transmission of SARS-CoV-2. Experimental infections conducted by several research groups have shown that monkeys, hamsters, ferrets, cats, tree shrews, transgenic mice and fruit bats were permissive, while dogs, pigs and poultry were resistant. There is an urgent need to understand the zoonotic potential of different viruses in animals, particularly in bats, before they transmit to humans. Vaccines or antivirals against SARS-CoV-2 should be evaluated not only for humans, but also for the protection of companion animals (particularly cats) and susceptible zoo and farm animals.
Collapse
Affiliation(s)
- Ahmed S. Abdel-Moneim
- Microbiology Department, Virology Division, College of Medicine, Taif University, Al-Taif 21944, Saudi Arabia; or
- Virology Department, Faculty of Veterinary Medicine, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Elsayed M. Abdelwhab
- Institute of Molecular Virology and Cell Biology, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald-Insel Riems, Germany
| |
Collapse
|
36
|
Jermiin LS, Catullo RA, Holland BR. A new phylogenetic protocol: dealing with model misspecification and confirmation bias in molecular phylogenetics. NAR Genom Bioinform 2020; 2:lqaa041. [PMID: 33575594 PMCID: PMC7671319 DOI: 10.1093/nargab/lqaa041] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 05/18/2020] [Accepted: 06/04/2020] [Indexed: 12/15/2022] Open
Abstract
Molecular phylogenetics plays a key role in comparative genomics and has increasingly significant impacts on science, industry, government, public health and society. In this paper, we posit that the current phylogenetic protocol is missing two critical steps, and that their absence allows model misspecification and confirmation bias to unduly influence phylogenetic estimates. Based on the potential offered by well-established but under-used procedures, such as assessment of phylogenetic assumptions and tests of goodness of fit, we introduce a new phylogenetic protocol that will reduce confirmation bias and increase the accuracy of phylogenetic estimates.
Collapse
Affiliation(s)
- Lars S Jermiin
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Biology & Environment Science, University College Dublin, Belfield, Dublin 4, Ireland
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Renee A Catullo
- CSIRO Land & Water, Canberra, ACT 2601, Australia
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia
- School of Science and Health & Hawkesbury Institute of the Environment, Western Sydney University, Penrith, NSW 2751, Australia
| | - Barbara R Holland
- School of Natural Sciences, University of Tasmania, Hobart, TAS 7001, Australia
| |
Collapse
|
37
|
|
38
|
Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes. mSphere 2020. [PMID: 32376697 DOI: 10.1101/2020.02.08.939660] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023] Open
Abstract
In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265-269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270-273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.
Collapse
Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nimit Jain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Massa J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
39
|
Wahba L, Jain N, Fire AZ, Shoura MJ, Artiles KL, McCoy MJ, Jeong DE. An Extensive Meta-Metagenomic Search Identifies SARS-CoV-2-Homologous Sequences in Pangolin Lung Viromes. mSphere 2020; 5:e00160-20. [PMID: 32376697 PMCID: PMC7203451 DOI: 10.1128/msphere.00160-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/24/2020] [Indexed: 12/21/2022] Open
Abstract
In numerous instances, tracking the biological significance of a nucleic acid sequence can be augmented through the identification of environmental niches in which the sequence of interest is present. Many metagenomic data sets are now available, with deep sequencing of samples from diverse biological niches. While any individual metagenomic data set can be readily queried using web-based tools, meta-searches through all such data sets are less accessible. In this brief communication, we demonstrate such a meta-metagenomic approach, examining close matches to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in all high-throughput sequencing data sets in the NCBI Sequence Read Archive accessible with the "virome" keyword. In addition to the homology to bat coronaviruses observed in descriptions of the SARS-CoV-2 sequence (F. Wu, S. Zhao, B. Yu, Y. M. Chen, et al., Nature 579:265-269, 2020, https://doi.org/10.1038/s41586-020-2008-3; P. Zhou, X. L. Yang, X. G. Wang, B. Hu, et al., Nature 579:270-273, 2020, https://doi.org/10.1038/s41586-020-2012-7), we note a strong homology to numerous sequence reads in metavirome data sets generated from the lungs of deceased pangolins reported by Liu et al. (P. Liu, W. Chen, and J. P. Chen, Viruses 11:979, 2019, https://doi.org/10.3390/v11110979). While analysis of these reads indicates the presence of a similar viral sequence in pangolin lung, the similarity is not sufficient to either confirm or rule out a role for pangolins as an intermediate host in the recent emergence of SARS-CoV-2. In addition to the implications for SARS-CoV-2 emergence, this study illustrates the utility and limitations of meta-metagenomic search tools in effective and rapid characterization of potentially significant nucleic acid sequences.IMPORTANCE Meta-metagenomic searches allow for high-speed, low-cost identification of potentially significant biological niches for sequences of interest.
Collapse
Affiliation(s)
- Lamia Wahba
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Nimit Jain
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Andrew Z Fire
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Massa J Shoura
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Karen L Artiles
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew J McCoy
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Dae-Eun Jeong
- Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| |
Collapse
|
40
|
Jacob JJ, Vasudevan K, Veeraraghavan B, Iyadurai R, Gunasekaran K. Genomic evolution of severe acute respiratory syndrome Coronavirus 2 in India and vaccine impact. Indian J Med Microbiol 2020; 38:210-212. [PMID: 32883935 PMCID: PMC7709607 DOI: 10.4103/ijmm.ijmm_20_303] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 07/04/2020] [Accepted: 07/27/2020] [Indexed: 12/28/2022]
Abstract
Recent emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and subsequent containment procedures have impacted the world as never seen before. Therefore, there is considerable curiosity about the genome evolution related to the origin, transmission and vaccine impact of this virus. We have analysed genome sequences of SARS-CoV-2 isolated from Indian patients to gain an in-depth understanding of genomic evolution and transmission in India. Phylogenetic analysis and mutation profiling revealed major lineages being evolved by characteristic mutations. As the mutation frequency in spike protein is comparatively lesser, the candidate vaccines expected to have wide coverage worldwide including India.
Collapse
MESH Headings
- Animals
- Antigens, Viral/genetics
- Antigens, Viral/immunology
- Antigens, Viral/metabolism
- Betacoronavirus/classification
- Betacoronavirus/genetics
- Betacoronavirus/immunology
- Betacoronavirus/pathogenicity
- COVID-19
- COVID-19 Vaccines
- Chiroptera/virology
- Coronavirus Infections/epidemiology
- Coronavirus Infections/genetics
- Coronavirus Infections/immunology
- Coronavirus Infections/prevention & control
- Coronavirus Infections/transmission
- Disease Reservoirs/virology
- Eutheria/virology
- Evolution, Molecular
- Genome, Viral
- Humans
- India/epidemiology
- Mutation
- Pandemics/prevention & control
- Phylogeny
- Pneumonia, Viral/epidemiology
- Pneumonia, Viral/immunology
- Pneumonia, Viral/prevention & control
- Pneumonia, Viral/transmission
- SARS-CoV-2
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Viral Vaccines/biosynthesis
- Viral Vaccines/genetics
- Viral Vaccines/immunology
Collapse
Affiliation(s)
- Jobin John Jacob
- Division of Molecular Biology and Translational Bioinformatics, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Division of Molecular Biology and Translational Bioinformatics, Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Hilda Lazarus Core Research Chair, Christian Medical College, Vellore, Tamil Nadu, India
| | - Ramya Iyadurai
- Department of General Medicine, Unit V, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthik Gunasekaran
- Department of General Medicine, Unit V, Christian Medical College, Vellore, Tamil Nadu, India
| |
Collapse
|
41
|
Affiliation(s)
- M. Brock Fenton
- Department of Biology, University of Western Ontario, London, ON N6A 5B7, Canada
| | - Samira Mubareka
- Department of Microbiology and Division of Infectious Diseases, Sunnybrook Health Sciences Centre and Research Institute, 2075 Bayview Avenue, Room B1 03, Toronto, ON M4N 3M5, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, ON M5S 1A1, Canada
| | - Susan M. Tsang
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
- Mammalogy Section, National Museum of the Philippines, 1000 Manila, Philippines
| | - Nancy B. Simmons
- Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY 10024, USA
| | - Daniel J. Becker
- Department of Biology, Indiana University, Bloomington, IN 47405, USA
| |
Collapse
|