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Wei L, Song L, Dunker AK, Foster JA, Uversky VN, Goh GKM. A Comparative Experimental and Computational Study on the Nature of the Pangolin-CoV and COVID-19 Omicron. Int J Mol Sci 2024; 25:7537. [PMID: 39062780 PMCID: PMC11277539 DOI: 10.3390/ijms25147537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 06/28/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024] Open
Abstract
The relationship between pangolin-CoV and SARS-CoV-2 has been a subject of debate. Further evidence of a special relationship between the two viruses can be found by the fact that all known COVID-19 viruses have an abnormally hard outer shell (low M disorder, i.e., low content of intrinsically disordered residues in the membrane (M) protein) that so far has been found in CoVs associated with burrowing animals, such as rabbits and pangolins, in which transmission involves virus remaining in buried feces for a long time. While a hard outer shell is necessary for viral survival, a harder inner shell could also help. For this reason, the N disorder range of pangolin-CoVs, not bat-CoVs, more closely matches that of SARS-CoV-2, especially when Omicron is included. The low N disorder (i.e., low content of intrinsically disordered residues in the nucleocapsid (N) protein), first observed in pangolin-CoV-2017 and later in Omicron, is associated with attenuation according to the Shell-Disorder Model. Our experimental study revealed that pangolin-CoV-2017 and SARS-CoV-2 Omicron (XBB.1.16 subvariant) show similar attenuations with respect to viral growth and plaque formation. Subtle differences have been observed that are consistent with disorder-centric computational analysis.
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Affiliation(s)
- Lai Wei
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100089, China;
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100089, China;
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
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2
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Xia LY, Wang XF, Cui XM, Zhang YM, Wang ZF, Li ET, Fan CF, Song K, Li YG, Ye RZ, Li FX, Zhu DY, Zhang J, Shi ZZ, Zhang MZ, Li LJ, Shen SJ, Jin S, Zhang YW, Fu WG, Zhao L, Wang WH, Wang TC, Wang YC, Jiang JF, Hu YL, Jia N, Gao YW, Cao WC. Characterization of a pangolin SARS-CoV-2-related virus isolate that uses the human ACE2 receptor. SCIENCE CHINA. LIFE SCIENCES 2024; 67:1502-1513. [PMID: 38478297 DOI: 10.1007/s11427-023-2484-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/08/2023] [Indexed: 06/19/2024]
Abstract
Various SARS-CoV-2-related coronaviruses have been increasingly identified in pangolins, showing a potential threat to humans. Here we report the infectivity and pathogenicity of the SARS-CoV-2-related virus, PCoV-GX/P2V, which was isolated from a Malayan pangolin (Manis javanica). PCoV-GX/P2V could grow in human hepatoma, colorectal adenocarcinoma cells, and human primary nasal epithelial cells. It replicated more efficiently in cells expressing human angiotensin-converting enzyme 2 (hACE2) as SARS-CoV-2 did. After intranasal inoculation to the hACE2-transgenic mice, PCoV-GX/P2V not only replicated in nasal turbinate and lungs, but also caused interstitial pneumonia, characterized by infiltration of mixed inflammatory cells and multifocal alveolar hemorrhage. Existing population immunity established by SARS-CoV-2 infection and vaccination may not protect people from PCoV-GX/P2V infection. These findings further verify the hACE2 utility of PCoV-GX/P2V by in vivo experiments using authentic viruses and highlight the importance for intensive surveillance to prevent possible cross-species transmission.
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Affiliation(s)
- Luo-Yuan Xia
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Xue-Feng Wang
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Xiao-Ming Cui
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China
| | - Yi-Ming Zhang
- Changchun Veterinary Research Institute, Changchun, 130122, China
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China
| | - Zhen-Fei Wang
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - En-Tao Li
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Chang-Fa Fan
- Division of Animal Model Research, Institute for Laboratory Animal Resources, National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Ke Song
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Yuan-Guo Li
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Run-Ze Ye
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Fang-Xu Li
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Dai-Yun Zhu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Jie Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | | | - Ming-Zhu Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Liang-Jing Li
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Shi-Jing Shen
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Song Jin
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Ya-Wei Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
| | - Wei-Guang Fu
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Lin Zhao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Wen-Hao Wang
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - Tie-Cheng Wang
- Changchun Veterinary Research Institute, Changchun, 130122, China
| | - You-Chun Wang
- National Institutes for Food and Drug Control, Beijing, 102629, China
| | - Jia-Fu Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China
| | - Yan-Ling Hu
- Life Sciences Institute, Guangxi Medical University, Nanning, 530020, China
| | - Na Jia
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China.
| | - Yu-Wei Gao
- Changchun Veterinary Research Institute, Changchun, 130122, China.
| | - Wu-Chun Cao
- Institute of EcoHealth, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, China.
- Research Unit of Discovery and Tracing of Natural Focus Diseases, Chinese Academy of Medical Sciences, Beijing, 100071, China.
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3
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Lu S, Luo S, Liu C, Li M, An X, Li M, Hou J, Fan H, Mao P, Tong Y, Song L. Induction of significant neutralizing antibodies against SARS-CoV-2 by a highly attenuated pangolin coronavirus variant with a 104nt deletion at the 3'-UTR. Emerg Microbes Infect 2023; 12:2151383. [PMID: 36453209 PMCID: PMC9769135 DOI: 10.1080/22221751.2022.2151383] [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] [Indexed: 12/05/2022]
Abstract
SARS-CoV-2 related coronaviruses (SARS-CoV-2r) from Guangdong and Guangxi pangolins have been implicated in the emergence of SARS-CoV-2 and future pandemics. We previously reported the culture of a SARS-CoV-2r GX_P2V from Guangxi pangolins. Here we report the GX_P2V isolate rapidly adapted to Vero cells by acquiring two genomic mutations: an alanine to valine substitution in the nucleoprotein and a 104-nucleotide deletion in the hypervariable region (HVR) of the 3'-terminus untranslated region (3'-UTR). We further report the characterization of the GX_P2V variant (renamed GX_P2V(short_3UTR)) in in vitro and in vivo infection models. In cultured Vero, BGM and Calu-3 cells, GX_P2V(short_3UTR) had similar robust replication kinetics, and consistently produced minimum cell damage. GX_P2V(short_3UTR) infected golden hamsters and BALB/c mice but was highly attenuated. Golden hamsters infected intranasally had a short duration of productive infection in pulmonary, not extrapulmonary, tissues. These productive infections induced neutralizing antibodies against pseudoviruses of GX_P2V and SARS-CoV-2. Collectively, our data show that the GX_P2V(short_3UTR) is highly attenuated in in vitro and in vivo infection models. Attenuation of the variant is likely partially due to the 104-nt deletion in the HVR in the 3'-UTR. This study furthers our understanding of pangolin coronaviruses pathogenesis and provides novel insights for the design of live attenuated vaccines against SARS-CoV-2.
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Affiliation(s)
- Shanshan Lu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Shengdong Luo
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Chang Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Muli Li
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, People’s Republic of China
| | - Xiaoping An
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Mengzhe Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Jun Hou
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Huahao Fan
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China,Huahao Fan Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Panyong Mao
- Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China,Panyong Mao Department of Infectious Diseases, Fifth Medical Center of Chinese PLA General Hospital, Beijing, People’s Republic of China
| | - Yigang Tong
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China,Yigang Tong Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
| | - Lihua Song
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China, Lihua Song Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, People’s Republic of China
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4
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A Study on the Nature of SARS-CoV-2 Using the Shell Disorder Models: Reproducibility, Evolution, Spread, and Attenuation. Biomolecules 2022; 12:biom12101353. [PMID: 36291562 PMCID: PMC9599796 DOI: 10.3390/biom12101353] [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: 08/23/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 12/03/2022] Open
Abstract
The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID—percentage of intrinsic disorder—of the membrane protein M, PIDM) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles in the lungs and bronchial tissues, respectively, as there is a greater level of mucus in the bronchi. The other observation revealed that there are lower viral loads in 2017-pangolin-CoV, which is predicted to have similarly low PIDN as Omicron. The abnormally hard M, which is very rarely seen in coronaviruses, arose from the fecal–oral behaviors of pangolins via exposure to buried feces. Pangolins provide an environment for coronavirus (CoV) attenuation, which is seen in Omicron. Phylogenetic study using M shows that COVID-19-related bat-CoVs from Laos and Omicron are clustered in close proximity to pangolin-CoVs, which suggests the recurrence of interspecies transmissions. Hard M may have implications for long COVID-19, with immune systems having difficulty degrading viral proteins/particles.
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Islam A, Ferdous J, Islam S, Sayeed MA, Rahman MK, Saha O, Hassan MM, Shirin T. Transmission dynamics and susceptibility patterns of SARS-CoV-2 in domestic, farmed and wild animals: Sustainable One Health surveillance for conservation and public health to prevent future epidemics and pandemics. Transbound Emerg Dis 2022; 69:2523-2543. [PMID: 34694705 PMCID: PMC8662162 DOI: 10.1111/tbed.14356] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/14/2021] [Accepted: 10/17/2021] [Indexed: 12/11/2022]
Abstract
The exact origin of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and source of introduction into humans has not been established yet, though it might be originated from animals. Therefore, we conducted a study to understand the putative reservoirs, transmission dynamics, and susceptibility patterns of SARS-CoV-2 in animals. Rhinolophus bats are presumed to be natural progenitors of SARS-CoV-2-related viruses. Initially, pangolin was thought to be the source of spillover to humans, but they might be infected by human or other animal species. So, the virus spillover pathways to humans remain unknown. Human-to-animal transmission has been testified in pet, farmed, zoo and free-ranging wild animals. Infected animals can transmit the virus to other animals in natural settings like mink-to-mink and mink-to-cat transmission. Animal-to-human transmission is not a persistent pathway, while mink-to-human transmission continues to be illuminated. Multiple companions and captive wild animals were infected by an emerging alpha variant of concern (B.1.1.7 lineage) whereas Asiatic lions were infected by delta variant, (B.1.617.2). To date, multiple animal species - cat, ferrets, non-human primates, hamsters and bats - showed high susceptibility to SARS-CoV-2 in the experimental condition, while swine, poultry, cattle showed no susceptibility. The founding of SARS-CoV-2 in wild animal reservoirs can confront the control of the virus in humans and might carry a risk to the welfare and conservation of wildlife as well. We suggest vaccinating pets and captive animals to stop spillovers and spillback events. We recommend sustainable One Health surveillance at the animal-human-environmental interface to detect and prevent future epidemics and pandemics by Disease X.
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Affiliation(s)
- Ariful Islam
- EcoHealth AllianceNew YorkUnited States
- Centre for Integrative Ecology, School of Life and Environmental ScienceDeakin UniversityVictoriaAustralia
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Jinnat Ferdous
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Shariful Islam
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Abu Sayeed
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Md. Kaisar Rahman
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
| | - Otun Saha
- EcoHealth AllianceNew YorkUnited States
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
| | - Mohammad Mahmudul Hassan
- Faculty of Veterinary MedicineChattogram Veterinary and Animal Sciences UniversityChattogramBangladesh
| | - Tahmina Shirin
- Institute of EpidemiologyDisease Control and Research (IEDCR)DhakaBangladesh
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Dos Santos DA, Reynaga MC, González JC, Fontanarrosa G, Gultemirian MDL, Novillo A, Abdala V. Insights on the evolution of Coronavirinae in general, and SARS-CoV-2 in particular, through innovative biocomputational resources. PeerJ 2022; 10:e13700. [PMID: 35910777 PMCID: PMC9332319 DOI: 10.7717/peerj.13700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 06/17/2022] [Indexed: 01/17/2023] Open
Abstract
The structural proteins of coronaviruses portray critical information to address issues of classification, assembly constraints, and evolutionary pathways involving host shifts. We compiled 173 complete protein sequences from isolates belonging to the four genera of the subfamily Coronavirinae. We calculate a single matrix of viral distance as a linear combination of protein distances. The minimum spanning tree (MST) connecting the individuals captures the structure of their similarities. The MST re-capitulates the known phylogeny of Coronovirinae. Hosts were mapped onto the MST and we found a non-trivial concordance between host phylogeny and viral proteomic distance. We also study the chimerism in our dataset through computational simulations. We found evidence that structural units coming from loosely related hosts hardly give rise to feasible chimeras in nature. This work offers a fresh way to analyze features of SARS-CoV-2 and related viruses.
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Affiliation(s)
- Daniel Andrés Dos Santos
- Cátedra de Bioestadística, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina,Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina
| | - María Celina Reynaga
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina
| | - Juan Cruz González
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina
| | - Gabriela Fontanarrosa
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina
| | - María de Lourdes Gultemirian
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina,Cátedra de Química Inorgánica, Facultad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
| | - Agustina Novillo
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina
| | - Virginia Abdala
- Instituto de Biodiversidad Neotropical, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET) - Universidad Nacional de Tucumán (UNT), Yerba Buena, Tucuman, Argentina,Cátedra de Biología General y Metodología de las Ciencias, Facultadad de Ciencias Naturales e Instituto Miguel Lillo, Universidad Nacional de Tucumán, San Miguel de Tucumán, Tucumán, Argentina
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Shell Disorder Models Detect That Omicron Has Harder Shells with Attenuation but Is Not a Descendant of the Wuhan-Hu-1 SARS-CoV-2. Biomolecules 2022; 12:631. [PMID: 35625559 PMCID: PMC9139003 DOI: 10.3390/biom12050631] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/17/2022] [Accepted: 04/20/2022] [Indexed: 02/01/2023] Open
Abstract
Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%-lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer shell) among all CoVs. This is likely to be responsible for the higher contagiousness of SARS-CoV-2 and Omicron, since hard outer shell protects the virion from salivary/mucosal antimicrobial enzymes. Phylogenetic study using M reveals that Omicron branched off from an ancestor of the Wuhan-Hu-1 strain closely related to pangolin-CoVs. M, being evolutionarily conserved in COVID-19, is most ideal for COVID-19 phylogenetic study. Omicron may have been hiding among burrowing animals (e.g., pangolins) that provide optimal evolutionary environments for attenuation and increase shell hardness, which is essential for fecal-oral-respiratory transmission via buried feces. Incoming data support SDM e.g., the presence of fewer infectious particles in the lungs than in the bronchi upon infection.
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Affiliation(s)
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - James A. Foster
- Department of Biological Sciences, University of Idaho, Moscow, ID 83844, USA;
- Institute for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, ID 83844, USA
| | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia
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8
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Goh GKM, Dunker AK, Foster JA, Uversky VN. Computational, Experimental, and Clinical Evidence of a Specific but Peculiar Evolutionary Nature of (COVID-19) SARS-CoV-2. J Proteome Res 2022; 21:874-890. [PMID: 35142523 PMCID: PMC8864774 DOI: 10.1021/acs.jproteome.2c00001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Indexed: 11/30/2022]
Abstract
The shell disorder models have predicted that SARS-CoV-2 is of a specific but peculiar evolutionary nature. All coronaviruses (CoVs) closely related to SARS-CoV-2 have been found to have the hardest outer shells (M protein) among CoVs. This hard shell (low M percentage of intrinsic disorder (PID)) is associated with burrowing animals, for example, pangolins, and is believed to be responsible for the high contagiousness of SARS-CoV-2 because it will be more resistant to antimicrobial enzymes found in saliva/mucus. Incoming clinical and experimental data do support this along with a prediction based on another aspect of the shell (N, inner shell) disorder models that SARS-CoV-1 is more virulent than SARS-CoV-2 because SARS-CoV-2 produces fewer virus copies in vital organs even if large amounts of infections particles are shed orally and nasally. A phylogenetic study using M reveals a closer relationship of SARS-CoV to pangolin-CoVs than the bat-RaTG13 found in Yunnan, China. Previous studies may have been confused by recombinations that were poorly handled. The shell disorder models suggest that a pangolin-CoV strain may have entered the human population in 2017 or before as an attenuated virus, which could explain why SARS-CoV is found to be highly adapted to humans.
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Affiliation(s)
| | - A. Keith Dunker
- Center for Computational Biology and Bioinformatics,
Indiana University School of Medicine, Indianapolis, Indiana
46202, United States
| | - James A. Foster
- Department of Biological Sciences,
University of Idaho, Moscow, Idaho 83844, United
States
- Institute for Bioinformatics and Evolutionary Studies,
University of Idaho, Moscow, Idaho 83844, United
States
| | - Vladimir N. Uversky
- Department of Molecular Medicine, USF Health Byrd
Alzheimer’s Research Institute, Morsani College of Medicine,
University of South Florida, Tampa, Florida 33620,
United States
- Laboratory of New Methods in Biology, 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, Moscow Region 142290,
Russia
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9
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Caldera-Crespo LA, Paidas MJ, Roy S, Schulman CI, Kenyon NS, Daunert S, Jayakumar AR. Experimental Models of COVID-19. Front Cell Infect Microbiol 2022; 11:792584. [PMID: 35096645 PMCID: PMC8791197 DOI: 10.3389/fcimb.2021.792584] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/26/2021] [Indexed: 12/20/2022] Open
Abstract
COVID-19 is the most consequential pandemic of the 21st century. Since the earliest stage of the 2019-2020 epidemic, animal models have been useful in understanding the etiopathogenesis of SARS-CoV-2 infection and rapid development of vaccines/drugs to prevent, treat or eradicate SARS-CoV-2 infection. Early SARS-CoV-1 research using immortalized in-vitro cell lines have aided in understanding different cells and receptors needed for SARS-CoV-2 infection and, due to their ability to be easily manipulated, continue to broaden our understanding of COVID-19 disease in in-vivo models. The scientific community determined animal models as the most useful models which could demonstrate viral infection, replication, transmission, and spectrum of illness as seen in human populations. Until now, there have not been well-described animal models of SARS-CoV-2 infection although transgenic mouse models (i.e. mice with humanized ACE2 receptors with humanized receptors) have been proposed. Additionally, there are only limited facilities (Biosafety level 3 laboratories) available to contribute research to aid in eventually exterminating SARS-CoV-2 infection around the world. This review summarizes the most successful animal models of SARS-CoV-2 infection including studies in Non-Human Primates (NHPs) which were found to be susceptible to infection and transmitted the virus similarly to humans (e.g., Rhesus macaques, Cynomolgus, and African Green Monkeys), and animal models that do not require Biosafety level 3 laboratories (e.g., Mouse Hepatitis Virus models of COVID-19, Ferret model, Syrian Hamster model). Balancing safety, mimicking human COVID-19 and robustness of the animal model, the Murine Hepatitis Virus-1 Murine model currently represents the most optimal model for SARS-CoV-2/COVID19 research. Exploring future animal models will aid researchers/scientists in discovering the mechanisms of SARS-CoV-2 infection and in identifying therapies to prevent or treat COVID-19.
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Affiliation(s)
- Luis A Caldera-Crespo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- St. George's University Graduate Medical Education Program, University Centre Grenada, West Indies, Grenada
| | - Michael J Paidas
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Carl I Schulman
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Norma Sue Kenyon
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Biomedical Engineering, University of Miami Miller School of Medicine, Miami, FL, United States
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of Medicine, Miami, FL, United States
- University of Miami Clinical and Translational Science Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Arumugam R Jayakumar
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
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Adhikari N, Banerjee S, Baidya SK, Ghosh B, Jha T. Ligand-based quantitative structural assessments of SARS-CoV-2 3CL pro inhibitors: An analysis in light of structure-based multi-molecular modeling evidences. J Mol Struct 2021; 1251:132041. [PMID: 34866654 PMCID: PMC8627846 DOI: 10.1016/j.molstruc.2021.132041] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 11/10/2021] [Accepted: 11/26/2021] [Indexed: 12/11/2022]
Abstract
Due to COVID-19, the whole world is undergoing a devastating situation, but treatment with no such drug candidates still has been established exclusively. In that context, 69 diverse chemicals with potential SARS-CoV-2 3CLpro inhibitory property were taken into consideration for building different internally and externally validated linear (SW-MLR and GA-MLR), non-linear (ANN and SVM) QSAR, and HQSAR models to identify important structural and physicochemical characters required for SARS-CoV-2 3CLpro inhibition. Importantly, 2-oxopyrrolidinyl methyl and benzylester functions, and methylene (hydroxy) sulphonic acid warhead group, were crucial for retaining higher SARS-CoV-2 3CLpro inhibition. These GA-MLR and HQSAR models were also applied to predict some already repurposed drugs. As per the GA-MLR model, curcumin, ribavirin, saquinavir, sepimostat, and remdesivir were found to be the potent ones, whereas according to the HQSAR model, lurasidone, saquinavir, lopinavir, elbasvir, and paritaprevir were the highly effective SARS-CoV-2 3CLpro inhibitors. The binding modes of those repurposed drugs were also justified by the molecular docking, molecular dynamics (MD) simulation, and binding energy calculations conducted by several groups of researchers. This current work, therefore, may be able to find out important structural parameters to accelerate the COVID-19 drug discovery processes in the future.
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Affiliation(s)
- Nilanjan Adhikari
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Suvankar Banerjee
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Sandip Kumar Baidya
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
| | - Balaram Ghosh
- Epigenetic Research Laboratory, Birla Institute of Technology and Science-Pilani Hyderabad Campus, Shamirpet, Hyderabad, India, 500078
| | - Tarun Jha
- Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, Jadavpur University, Kolkata 700032, India
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Caetano-Anollés K, Hernandez N, Mughal F, Tomaszewski T, Caetano-Anollés G. The seasonal behaviour of COVID-19 and its galectin-like culprit of the viral spike. METHODS IN MICROBIOLOGY 2021; 50:27-81. [PMID: 38620818 PMCID: PMC8590929 DOI: 10.1016/bs.mim.2021.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Seasonal behaviour is an attribute of many viral diseases. Like other 'winter' RNA viruses, infections caused by the causative agent of COVID-19, SARS-CoV-2, appear to exhibit significant seasonal changes. Here we discuss the seasonal behaviour of COVID-19, emerging viral phenotypes, viral evolution, and how the mutational landscape of the virus affects the seasonal attributes of the disease. We propose that the multiple seasonal drivers behind infectious disease spread (and the spread of COVID-19 specifically) are in 'trade-off' relationships and can be better described within a framework of a 'triangle of viral persistence' modulated by the environment, physiology, and behaviour. This 'trade-off' exists as one trait cannot increase without a decrease in another. We also propose that molecular components of the virus can act as sensors of environment and physiology, and could represent molecular culprits of seasonality. We searched for flexible protein structures capable of being modulated by the environment and identified a galectin-like fold within the N-terminal domain of the spike protein of SARS-CoV-2 as a potential candidate. Tracking the prevalence of mutations in this structure resulted in the identification of a hemisphere-dependent seasonal pattern driven by mutational bursts. We propose that the galectin-like structure is a frequent target of mutations because it helps the virus evade or modulate the physiological responses of the host to further its spread and survival. The flexible regions of the N-terminal domain should now become a focus for mitigation through vaccines and therapeutics and for prediction and informed public health decision making.
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Affiliation(s)
| | - Nicolas Hernandez
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Fizza Mughal
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Tre Tomaszewski
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
| | - Gustavo Caetano-Anollés
- Evolutionary Bioinformatics Laboratory, Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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Kaneko S, Takasawa K, Asada K, Shinkai N, Bolatkan A, Yamada M, Takahashi S, Machino H, Kobayashi K, Komatsu M, Hamamoto R. Epigenetic Mechanisms Underlying COVID-19 Pathogenesis. Biomedicines 2021; 9:1142. [PMID: 34572329 PMCID: PMC8466119 DOI: 10.3390/biomedicines9091142] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/27/2021] [Accepted: 08/31/2021] [Indexed: 12/11/2022] Open
Abstract
In 2019, a novel severe acute respiratory syndrome called coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was reported and was declared a pandemic by the World Health Organization (WHO) in March 2020. With the advancing development of COVID-19 vaccines and their administration globally, it is expected that COVID-19 will converge in the future; however, the situation remains unpredictable because of a series of reports regarding SARS-CoV-2 variants. Currently, there are still few specific effective treatments for COVID-19, as many unanswered questions remain regarding the pathogenic mechanism of COVID-19. Continued elucidation of COVID-19 pathogenic mechanisms is a matter of global importance. In this regard, recent reports have suggested that epigenetics plays an important role; for instance, the expression of angiotensin I converting enzyme 2 (ACE2) receptor, an important factor in human infection with SARS-CoV-2, is epigenetically regulated; further, DNA methylation status is reported to be unique to patients with COVID-19. In this review, we focus on epigenetic mechanisms to provide a new molecular framework for elucidating the pathogenesis of SARS-CoV-2 infection in humans and of COVID-19, along with the possibility of new diagnostic and therapeutic strategies.
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Affiliation(s)
- Syuzo Kaneko
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Takasawa
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ken Asada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Norio Shinkai
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
| | - Amina Bolatkan
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Masayoshi Yamada
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- National Cancer Center Hospital, Department of Endoscopy, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
| | - Satoshi Takahashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Hidenori Machino
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Kazuma Kobayashi
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Masaaki Komatsu
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
| | - Ryuji Hamamoto
- Division of Medical AI Research and Development, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan; (S.K.); (K.T.); (K.A.); (N.S.); (A.B.); (M.Y.); (S.T.); (H.M.); (K.K.); (M.K.)
- Cancer Translational Research Team, RIKEN Center for Advanced Intelligence Project, 1-4-1 Nihonbashi, Chuo-ku, Tokyo 103-0027, Japan
- Department of NCC Cancer Science, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8510, Japan
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Shao L, Ge S, Jones T, Santosh M, Silva LFO, Cao Y, Oliveira MLS, Zhang M, BéruBé K. The role of airborne particles and environmental considerations in the transmission of SARS-CoV-2. GEOSCIENCE FRONTIERS 2021; 12:101189. [PMID: 38620834 PMCID: PMC8020609 DOI: 10.1016/j.gsf.2021.101189] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 03/15/2021] [Accepted: 03/17/2021] [Indexed: 05/06/2023]
Abstract
Corona Virus Disease 2019 (COVID-19) caused by the novel coronavirus, results in an acute respiratory condition coronavirus 2 (SARS-CoV-2) and is highly infectious. The recent spread of this virus has caused a global pandemic. Currently, the transmission routes of SARS-CoV-2 are being established, especially the role of environmental transmission. Here we review the environmental transmission routes and persistence of SARS-CoV-2. Recent studies have established that the transmission of this virus may occur, amongst others, in the air, water, soil, cold-chain, biota, and surface contact. It has also been found that the survival potential of the SARS-CoV-2 virus is dependent on different environmental conditions and pollution. Potentially important pathways include aerosol and fecal matter. Particulate matter may also be a carrier for SARS-CoV-2. Since microscopic particles can be easily absorbed by humans, more attention must be focused on the dissemination of these particles. These considerations are required to evolve a theoretical platform for epidemic control and to minimize the global threat from future epidemics.
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Affiliation(s)
- Longyi Shao
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
- College of Geoscience and Surveying Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Shuoyi Ge
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
- College of Geoscience and Surveying Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Tim Jones
- School of Earth and Environmental Sciences, Cardiff University, Museum Avenue, Cardiff, CF10 3YE, UK
| | - M Santosh
- School of Earth Sciences and Resources, China University of Geosciences Beijing, Beijing 100083, China
- Department of Earth Science, University of Adelaide, Adelaide, SA 5005, Australia
| | - Luis F O Silva
- Department of Civil and Environmental, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlántico, Colombia
| | - Yaxin Cao
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
- College of Geoscience and Surveying Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Marcos L S Oliveira
- Department of Civil and Environmental, Universidad de la Costa, Calle 58 #55-66, 080002 Barranquilla, Atlántico, Colombia
- Departamento de Ingeniería Civil y Arquitectura, Universidad de Lima, Avenida Javier Prado Este 4600 - Santiago de, Surco 1503, Peru
| | - Mengyuan Zhang
- State Key Laboratory of Coal Resources and Safe Mining, China University of Mining and Technology (Beijing), Beijing 100083, China
- College of Geoscience and Surveying Engineering, China University of Mining and Technology (Beijing), Beijing 100083, China
| | - Kelly BéruBé
- School of Biosciences, Cardiff University, Museum Avenue, Cardiff CF10 3AX, Wales, UK
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Bora I, Gogoi S, Venkatasubramanian V, Mathew R, Mohindra R. Persistence of SARS-COV-2 in body fluids: a bystander or whistle blower. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 12:370-375. [PMID: 33603990 PMCID: PMC7867692 DOI: 10.18502/ijm.v12i5.4596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The novel Coronavirus COVID-19 is wrecking a havoc across the globe and has been declared as a pandemic by WHO. Apart from transmission and shedding of the virus through respiratory secretions in the form of droplets (mainly), several studies have shown the presence of the virus in various samples such as stool, urine and occasionally in blood, semen, tears and breastmilk. Whereas government authority guidelines consider a person as cured from COVID-19 when along with clinical improvement no more virus can be detected primarily on respiratory samples along with clinical improvement; the persistence of the virus in these body fluids even after clinical recovery and negative RT-PCR test results on respiratory samples, has raised many questions about the elusive nature of this novel virus along with the possibility of other routes of transmission of this virus in the community. Although studies performed till now across the globe on persistence of SARSCOV-2 in various body fluids are sparse, in this review we would like to present and analyse the results of those studies performed globally on the aforesaid topic to get a better insight of this side of the COVID-19 story.
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Affiliation(s)
- Ishani Bora
- Department of Virology, Postgraduate Institute of Medical Education & Research, Chandigarh, India
| | - Sanjib Gogoi
- Department of Microbiology, Lady Hardinge Medical College, New Delhi, India
| | | | - Roshan Mathew
- Department of Emergency Medicine, All India Institute of Medical Sciences, New Delhi, India
| | - Ritin Mohindra
- Department of Internal Medicine, Postgraduate Institute of Medical Education & Research, Chandigarh, India
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15
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Hedman HD, Krawczyk E, Helmy YA, Zhang L, Varga C. Host Diversity and Potential Transmission Pathways of SARS-CoV-2 at the Human-Animal Interface. Pathogens 2021; 10:180. [PMID: 33567598 PMCID: PMC7915269 DOI: 10.3390/pathogens10020180] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 02/07/2023] Open
Abstract
Emerging infectious diseases present great risks to public health. The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus disease 2019 (COVID-19), has become an urgent public health issue of global concern. It is speculated that the virus first emerged through a zoonotic spillover. Basic research studies have suggested that bats are likely the ancestral reservoir host. Nonetheless, the evolutionary history and host susceptibility of SARS-CoV-2 remains unclear as a multitude of animals has been proposed as potential intermediate or dead-end hosts. SARS-CoV-2 has been isolated from domestic animals, both companion and livestock, as well as in captive wildlife that were in close contact with human COVID-19 cases. Currently, domestic mink is the only known animal that is susceptible to a natural infection, develop severe illness, and can also transmit SARS-CoV-2 to other minks and humans. To improve foundational knowledge of SARS-CoV-2, we are conducting a synthesis review of its host diversity and transmission pathways. To mitigate this COVID-19 pandemic, we strongly advocate for a systems-oriented scientific approach that comprehensively evaluates the transmission of SARS-CoV-2 at the human and animal interface.
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Affiliation(s)
- Hayden D. Hedman
- Summit County Local Public Health Agency, Summit County, Frisco, CO 80443, USA;
| | - Eric Krawczyk
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, IL 60612, USA;
| | - Yosra A. Helmy
- Food Animal Health Research Program, Department of Veterinary Preventive Medicine, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, USA;
| | - Lixin Zhang
- Department of Epidemiology and Biostatistics, Michigan State University, East Lansing, MI 48824, USA;
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA
| | - Csaba Varga
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois Urbana-Champaign, Urbana, IL 61802, USA
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Ozga D, Krupa S, Witt P, Mędrzycka-Dąbrowska W. Nursing Interventions to Prevent Delirium in Critically Ill Patients in the Intensive Care Unit during the COVID19 Pandemic-Narrative Overview. Healthcare (Basel) 2020; 8:healthcare8040578. [PMID: 33371277 PMCID: PMC7766119 DOI: 10.3390/healthcare8040578] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/11/2020] [Accepted: 12/13/2020] [Indexed: 01/08/2023] Open
Abstract
It has become a standard measure in recent years to utilise evidence-based practice, which is associated with a greater need to implement and use advanced, reliable methods of summarising the achievements of various scientific disciplines, including such highly specialised approaches as personalised medicine. The aim of this paper was to discuss the current state of knowledge related to improvements in "nursing" involving management of delirium in intensive care units during the SARS-CoV-2 pandemic. This narrative review summarises the current knowledge concerning the challenges associated with assessment of delirium in patients with COVID-19 by ICU nurses, and the role and tasks in the personalised approach to patients with COVID-19.
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Affiliation(s)
- Dorota Ozga
- Institute of Health Sciences, Medical College of Rzeszow University, 35-310 Rzeszow, Poland; (D.O.); (S.K.)
| | - Sabina Krupa
- Institute of Health Sciences, Medical College of Rzeszow University, 35-310 Rzeszow, Poland; (D.O.); (S.K.)
| | - Paweł Witt
- Department of Pediatric Anesthesiology and Intensive Care, Medical University of Warsaw, 02-091 Warszawa, Poland;
| | - Wioletta Mędrzycka-Dąbrowska
- Department of Anaesthesiology Nursing & Intensive Care, Medical University in Gdansk, 80-211 Gdańsk, Poland
- Correspondence:
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Morphogenetic (Mucin Expression) as Well as Potential Anti-Corona Viral Activity of the Marine Secondary Metabolite Polyphosphate on A549 Cells. Mar Drugs 2020; 18:md18120639. [PMID: 33327522 PMCID: PMC7764923 DOI: 10.3390/md18120639] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 12/14/2022] Open
Abstract
The mucus layer of the nasopharynx and bronchial epithelium has a barrier function against inhaled pathogens such as the coronavirus SARS-CoV-2. We recently found that inorganic polyphosphate (polyP), a physiological, metabolic energy (ATP)-providing polymer released from blood platelets, blocks the binding of the receptor binding domain (RBD) to the cellular ACE2 receptor in vitro. PolyP is a marine natural product and is abundantly present in marine bacteria. Now, we have approached the in vivo situation by studying the effect of polyP on the human alveolar basal epithelial A549 cells in a mucus-like mucin environment. These cells express mucins as well as the ectoenzymes alkaline phosphatase (ALP) and adenylate kinase (ADK), which are involved in the extracellular production of ATP from polyP. Mucin, integrated into a collagen-based hydrogel, stimulated cell growth and attachment. The addition of polyP to the hydrogel significantly increased cell attachment and also the expression of the membrane-tethered mucin MUC1 and the secreted mucin MUC5AC. The increased synthesis of MUC1 was also confirmed by immunostaining. This morphogenetic effect of polyP was associated with a rise in extracellular ATP level. We conclude that the nontoxic and non-immunogenic polymer polyP could possibly also exert a protective effect against SARS-CoV-2-cell attachment; first, by stimulating the innate antiviral response by strengthening the mucin barrier with its antimicrobial proteins, and second, by inhibiting virus attachment to the cells, as deduced from the reduction in the strength of binding between the viral RBD and the cellular ACE2 receptor.
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The Role of Protein Disorder in Nuclear Transport and in Its Subversion by Viruses. Cells 2020; 9:cells9122654. [PMID: 33321790 PMCID: PMC7764567 DOI: 10.3390/cells9122654] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 12/08/2020] [Accepted: 12/08/2020] [Indexed: 12/12/2022] Open
Abstract
The transport of host proteins into and out of the nucleus is key to host function. However, nuclear transport is restricted by nuclear pores that perforate the nuclear envelope. Protein intrinsic disorder is an inherent feature of this selective transport barrier and is also a feature of the nuclear transport receptors that facilitate the active nuclear transport of cargo, and the nuclear transport signals on the cargo itself. Furthermore, intrinsic disorder is an inherent feature of viral proteins and viral strategies to disrupt host nucleocytoplasmic transport to benefit their replication. In this review, we highlight the role that intrinsic disorder plays in the nuclear transport of host and viral proteins. We also describe viral subversion mechanisms of the host nuclear transport machinery in which intrinsic disorder is a feature. Finally, we discuss nuclear import and export as therapeutic targets for viral infectious disease.
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Goh GKM, Dunker AK, Foster JA, Uversky VN. A Novel Strategy for the Development of Vaccines for SARS-CoV-2 (COVID-19) and Other Viruses Using AI and Viral Shell Disorder. J Proteome Res 2020; 19:4355-4363. [PMID: 33006287 PMCID: PMC7640981 DOI: 10.1021/acs.jproteome.0c00672] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Indexed: 12/29/2022]
Abstract
A model that predicts levels of coronavirus (CoV) respiratory and fecal-oral transmission potentials based on the shell disorder has been built using neural network (artificial intelligence, AI) analysis of the percentage of disorder (PID) in the nucleocapsid, N, and membrane, M, proteins of the inner and outer viral shells, respectively. Using primarily the PID of N, SARS-CoV-2 is grouped as having intermediate levels of both respiratory and fecal-oral transmission potentials. Related studies, using similar methodologies, have found strong positive correlations between virulence and inner shell disorder among numerous viruses, including Nipah, Ebola, and Dengue viruses. There is some evidence that this is also true for SARS-CoV-2 and SARS-CoV, which have N PIDs of 48% and 50%, and case-fatality rates of 0.5-5% and 10.9%, respectively. The underlying relationship between virulence and respiratory potentials has to do with the viral loads of vital organs and body fluids, respectively. Viruses can spread by respiratory means only if the viral loads in saliva and mucus exceed certain minima. Similarly, a patient is likelier to die when the viral load overwhelms vital organs. Greater disorder in inner shell proteins has been known to play important roles in the rapid replication of viruses by enhancing the efficiency pertaining to protein-protein/DNA/RNA/lipid bindings. This paper suggests a novel strategy in attenuating viruses involving comparison of disorder patterns of inner shells (N) of related viruses to identify residues and regions that could be ideal for mutation. The M protein of SARS-CoV-2 has one of the lowest M PID values (6%) in its family, and therefore, this virus has one of the hardest outer shells, which makes it resistant to antimicrobial enzymes in body fluid. While this is likely responsible for its greater contagiousness, the risks of creating an attenuated virus with a more disordered M are discussed.
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Affiliation(s)
| | - A. Keith Dunker
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - James A. Foster
- Department
of Biological Sciences, University of Idaho, Moscow, Idaho 83844, United States
- Institute
for Bioinformatics and Evolutionary Studies, University of Idaho, Moscow, Idaho 83844, United States
| | - Vladimir N. Uversky
- Department
of Molecular Medicine, USF Health Byrd Alzheimer’s Research
Institute, Morsani College of Medicine, University of South Florida, Tampa, Florida 33620, United States
- Laboratory
of New Methods in Biology, 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, Moscow region 142290, Russia
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Affiliation(s)
- Suman S. Thakur
- Proteomics and Cell Signaling, Lab
W110, Centre for Cellular & Molecular
Biology, Habsiguda, Uppal
Road, Hyderabad 500 007, Telangana, India
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Baviskar T, Raut D, Bhatt LK. Deciphering Vaccines for COVID-19: where do we stand today? Immunopharmacol Immunotoxicol 2020; 43:8-21. [PMID: 33054486 DOI: 10.1080/08923973.2020.1837867] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pneumonia of unknown etiology was detected in a few patients in Wuhan City, Hubei Province, China. The causative agent was named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by the World Health Organization (WHO). The disease caused by this virus was named as a new coronavirus disease: COVID-19. The disease has a global impact affecting more than 200 nations including the USA, India, Brazil, Russia, and Peru are the 5 most severely affected nations. The discovery of the genotype and phenotype of SARS-CoV-2 boosted the global efforts for the development of treatment options and vaccines for the COVID-19. As the transmission of the virus is rapid, to protect the global population, the development of an effective vaccine against the virus is very essential. The current review highlights the various platforms and technologies used globally for the development of the vaccine and also focuses on the current status of the vaccine candidates under development by organizations to combat the global threat of COVID-19 pandemic.
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Affiliation(s)
- Tushar Baviskar
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Dezaree Raut
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Lokesh Kumar Bhatt
- Department of Pharmacology, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
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