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Perlman S. A balance between innovation and biosafety. Proc Natl Acad Sci U S A 2024; 121:e2410451121. [PMID: 38976743 PMCID: PMC11260158 DOI: 10.1073/pnas.2410451121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024] Open
Affiliation(s)
- Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
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2
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Zhang F, Chai C, Niu R, Diao Y, Zhou Y, Zhang J, Feng L, Yao C, Wu Y, Ma Y, Zan X, Wang W. Genetic characterization of bovine coronavirus strain isolated in Inner Mongolia of China. BMC Vet Res 2024; 20:209. [PMID: 38760785 PMCID: PMC11102244 DOI: 10.1186/s12917-024-04046-3] [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: 02/21/2023] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Bovine coronavirus (BCoV) is implicated in severe diarrhea in calves and contributes to the bovine respiratory disease complex; it shares a close relationship with human coronavirus. Similar to other coronaviruses, remarkable variability was found in the genome and biology of the BCoV. In 2022, samples of feces were collected from a cattle farm. A virus was isolated from 7-day-old newborn calves. In this study, we present the genetic characteristics of a new BCoV isolate. The complete genomic, spike protein, and nucleocapsid protein gene sequences of the BCoV strain, along with those of other coronaviruses, were obtained from the GenBank database. Genetic analysis was conducted using MEGA7.0 and the Neighbor-Joining (NJ) method. The reference strains' related genes were retrieved from GenBank for comparison and analysis using DNAMAN. RESULTS The phylogenetic tree and whole genome consistency analysis showed that it belonged to the GIIb subgroup, which is epidemic in Asia and America, and was quite similar to the Chinese strains in the same cluster. Significantly, the S gene was highly consistent with QH1 (MH810151.1) isolated from yak. This suggests that the strain may have originated from interspecies transmission involving mutations of wild strains. The N gene was conserved and showed high sequence identity with the epidemic strains in China and the USA. CONCLUSIONS Genetic characterization suggests that the isolated strain could be a new mutant from a wild-type lineage, which is in the same cluster as most Chinese epidemic strains but on a new branch.
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Affiliation(s)
- Fan Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
- Veterinary Research Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, 010031, China
| | - Chunxia Chai
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Rui Niu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yun Diao
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yanyan Zhou
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Jinlong Zhang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Lin Feng
- Helinger County Bureau of Agriculture and Animal Husbandry, Hohhot, 011500, China
| | - Chunming Yao
- Helinger County Bureau of Agriculture and Animal Husbandry, Hohhot, 011500, China
| | - Youzhi Wu
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Yanhua Ma
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Xiaohui Zan
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China
| | - Wei Wang
- State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock, Inner Mongolia University, Hohhot, 010030, China.
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3
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Albright C, Van Egeren D, Thakur A, Chakravarty A, White LF, Stoddard M. Antibody escape, the risk of serotype formation, and rapid immune waning: Modeling the implications of SARS-CoV-2 immune evasion. PLoS One 2023; 18:e0292099. [PMID: 37851632 PMCID: PMC10584102 DOI: 10.1371/journal.pone.0292099] [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: 06/15/2023] [Accepted: 09/12/2023] [Indexed: 10/20/2023] Open
Abstract
As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of "endemicity" or "herd immunity." At this point, an array of viral strains has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antibody escape resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading strains that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control, and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
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Affiliation(s)
| | - Debra Van Egeren
- Stanford University School of Medicine, Stanford, CA, United States of America
| | - Aditya Thakur
- Boston University, Boston, MA, United States of America
| | | | - Laura F. White
- Boston University School of Public Health, Boston, MA, United States of America
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Abstract
The existence of coronaviruses has been known for many years. These viruses cause significant disease that primarily seems to affect agricultural species. Human coronavirus disease due to the 2002 outbreak of Severe Acute Respiratory Syndrome and the 2012 outbreak of Middle East Respiratory Syndrome made headlines; however, these outbreaks were controlled, and public concern quickly faded. This complacency ended in late 2019 when alarms were raised about a mysterious virus responsible for numerous illnesses and deaths in China. As we now know, this novel disease called Coronavirus Disease 2019 (COVID-19) was caused by Severe acute respiratory syndrome-related-coronavirus-2 (SARS-CoV-2) and rapidly became a worldwide pandemic. Luckily, decades of research into animal coronaviruses hastened our understanding of the genetics, structure, transmission, and pathogenesis of these viruses. Coronaviruses infect a wide range of wild and domestic animals, with significant economic impact in several agricultural species. Their large genome, low dependency on host cellular proteins, and frequent recombination allow coronaviruses to successfully cross species barriers and adapt to different hosts including humans. The study of the animal diseases provides an understanding of the virus biology and pathogenesis and has assisted in the rapid development of the SARS-CoV-2 vaccines. Here, we briefly review the classification, origin, etiology, transmission mechanisms, pathogenesis, clinical signs, diagnosis, treatment, and prevention strategies, including available vaccines, for coronaviruses that affect domestic, farm, laboratory, and wild animal species. We also briefly describe the coronaviruses that affect humans. Expanding our knowledge of this complex group of viruses will better prepare us to design strategies to prevent and/or minimize the impact of future coronavirus outbreaks.
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Key Words
- bcov, bovine coronavirus
- ccov, canine coronavirus
- cov(s), coronavirus(es)
- covid-19, coronavirus disease 2019
- crcov, canine respiratory coronavirus
- e, coronaviral envelope protein
- ecov, equine coronavirus
- fcov, feline coronavirus
- fipv, feline infectious peritonitis virus
- gfcov, guinea fowl coronavirus
- hcov, human coronavirus
- ibv, infectious bronchitis virus
- m, coronaviral membrane protein
- mers, middle east respiratory syndrome-coronavirus
- mhv, mouse hepatitis virus
- pedv, porcine epidemic diarrhea virus
- pdcov, porcine deltacoronavirus
- phcov, pheasant coronavirus
- phev, porcine hemagglutinating encephalomyelitis virus
- prcov, porcine respiratory coronavirus
- rt-pcr, reverse transcriptase polymerase chain reaction
- s, coronaviral spike protein
- sads-cov, swine acute diarrhea syndrome-coronavirus
- sars-cov, severe acute respiratory syndrome-coronavirus
- sars-cov-2, severe acute respiratory syndrome–coronavirus–2
- tcov, turkey coronavirus
- tgev, transmissible gastroenteritis virus
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Affiliation(s)
- Alfonso S Gozalo
- Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland;,
| | - Tannia S Clark
- Office of Laboratory Animal Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - David M Kurtz
- Comparative Medicine Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, Durham, North Carolina
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5
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Wali L, Karbiener M, Chou S, Kovtunyk V, Adonyi A, Gösler I, Contreras X, Stoeva D, Blaas D, Stöckl J, Kreil TR, Gualdoni GA, Gorki AD. Host-directed therapy with 2-Deoxy-D-glucose inhibits human rhinoviruses, endemic coronaviruses, and SARS-CoV-2. J Virus Erad 2022; 8:100305. [PMID: 36514716 PMCID: PMC9731833 DOI: 10.1016/j.jve.2022.100305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/30/2022] [Accepted: 12/01/2022] [Indexed: 12/13/2022] Open
Abstract
Rhinoviruses (RVs) and coronaviruses (CoVs) upregulate host cell metabolic pathways such as glycolysis to meet their bioenergetic demands for rapid multiplication. Using the glycolysis inhibitor 2-deoxy-D-glucose (2-DG), we assessed the dose-dependent inhibition of viral replication of minor- and major-receptor group RVs in epithelial cells. 2-DG disrupted RV infection cycle by inhibiting template negative-strand as well as genomic positive-strand RNA synthesis, resulting in less progeny virus and RV-mediated cell death. Assessment of 2-DG´s intracellular kinetics revealed that after a short-exposure to 2-DG, the active intermediate, 2-DG6P, is stored intracellularly for several hours. Finally, we confirmed the antiviral effect of 2-DG on pandemic SARS-CoV-2 and showed for the first time that 2-DG also reduces replication of endemic human coronaviruses (HCoVs). These results provide further evidence that 2-DG could be utilized as a broad-spectrum antiviral.
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Affiliation(s)
| | | | | | | | | | - Irene Gösler
- Center of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Austria
| | | | | | - Dieter Blaas
- Center of Medical Biochemistry, Max Perutz Labs, Vienna Biocenter, Medical University of Vienna, Austria
| | - Johannes Stöckl
- Institute of Immunology, Center of Pathophysiology, Immunology & Infectiology, Medical University of Vienna, Austria
| | - Thomas R. Kreil
- Global Pathogen Safety, Takeda Manufacturing Austria AG, Austria
| | | | - Anna-Dorothea Gorki
- G.ST Antivirals GmbH, Austria,Corresponding author. G.ST Antivirals GmbH, Doktor-Bohr-Gasse 7 (VBC6), 1030, Vienna, Austria
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6
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Abstract
The "Russian flu", which raged from 1889 to 1894, is considered as the first pandemic of the industrial era for which statistics have been collected. This planetary event started in Turkestan and hit the Russian Empire, before reaching all European countries, the United States of America, and the whole world. Contemporaries were surprised by its high contagiousness as evidenced by attack rates averaging 60% in urban populations, its rapid spread in successive waves circling the globe in a few months by rail and sea, and the tendency of the disease to relapse. Despite its low case-fatality rate (0.10%-0.28%), it is estimated to have caused one million deaths worldwide. On serological grounds, it is generally accepted that the causative agent of Russian influenza was Myxovirus influenzae, the virus identified for all influenza pandemics since the "Spanish flu" of 1918. In light of the Covid-19 pandemic, which has underscored the extraordinary epidemic potential of coronaviruses, this assumption has recently been questioned. Coronaviruses come from wild reservoirs (bats, rodents, birds, …). They induce respiratory symptoms mimicking influenza, possibly leading to respiratory distress with pneumonia. In addition to the Covid-19 pandemic, recent deadly and limited epidemics, such as SARS in 2002 and MERS in 2012, have occurred. Russian influenza presented as an influenza-like syndrome with clinical peculiarities (multivisceral and neurological involvement, skin rash, early iterative relapses), evoking some particularities of Covid-19. Four other coronaviruses circulating in the human population for decades (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1) have been found to be responsible for 15 to 30% of seasonal colds. All of these viruses are of animal origin. Recently, phylogenetic studies have revealed the genetic proximity between a bovine coronavirus BCoV and the human virus HCoV-OC43, indicating that the latter emerged around 1890, at the time of the Russian flu, when an epizootic was raging among cattle throughout Europe. Could the current human virus be the attenuated remnant that appeared after the Russian flu in 1894? Was there a coronavirus pandemic before Covid-19 ?
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7
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Non-SARS Coronaviruses in Individuals with Psychiatric Disorders. Curr Top Behav Neurosci 2022; 61:265-278. [PMID: 35947355 DOI: 10.1007/7854_2022_386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
BACKGROUND The pandemic caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) has highlighted the importance of coronaviruses in human health. Several seasonal, non-SARS Coronaviruses are endemic in most areas of the world. In a previous study, we found that the level of antibodies to these seasonal Coronaviruses was elevated in persons with a recent onset of psychosis. In the current study, the level of antibodies to seasonal Coronaviruses was compared between individuals with psychiatric disorders and a non-psychiatric comparison group. METHODS Participants (N = 195) were persons with a diagnosis of schizophrenia, bipolar disorder, major depressive disorder, or without a psychiatric disorder. Each participant had a blood sample drawn from which were measured IgG antibodies to the spike proteins in four non-SARS Coronaviruses, 229E, HKU1, NL63, and OC43, using a multiplex electrochemiluminescence assay. Linear regression models were employed to compare the levels of antibodies between each psychiatric group and the comparison group adjusting for demographic variables. Logistic regression models were employed to calculate the odds ratios associated with increased levels of antibodies to each seasonal Coronavirus based on the 50th percentile level of the comparison group. RESULTS The schizophrenia group had significantly increased levels of antibodies to the seasonal Coronaviruses OC43 and NL63. This group also had increased odds of having elevated antibody levels to OC43. The major depression group showed a significantly lower level of antibodies to Coronavirus 229E. There were no significant differences between any of the psychiatric groups and the comparison group in the levels of antibodies to seasonal Coronaviruses 229E or HKU1. CONCLUSIONS The elevated level of antibodies to OC43 and NL63 in the schizophrenia group indicates increased exposure to these agents and raises the possibility that Coronaviruses may contribute to the etiopathology of this disorder. The cause-and-effect relationship between seasonal Coronaviruses and psychiatric disorders should be the subject of additional investigations focusing on longitudinal cohort studies.
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8
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Al-Tawfiq JA, Chu DT, Hoang VT, Memish ZA. From Pandemicity to Endemicity: The Journey of SARS-CoV-2. J Epidemiol Glob Health 2022; 12:147-149. [PMID: 35704175 PMCID: PMC9198624 DOI: 10.1007/s44197-022-00046-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Affiliation(s)
- Jaffar A Al-Tawfiq
- Infectious Disease Unit, Specialty Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Dinh-Toi Chu
- Center for Biomedicine and Community Health, International School, Vietnam National University, Hanoi, Vietnam
| | - Van-Thuan Hoang
- Thai Binh University of Medicine and Pharmacy, Thai Binh, Vietnam
| | - Ziad A Memish
- Director Research and Innovation Centre, King Saud Medical City, Ministry of Health and College of Medicine, Alfaisal University, Riyadh, Kingdom of Saudi Arabia.
- Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, USA.
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9
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Wang C, Hesketh EL, Shamorkina TM, Li W, Franken PJ, Drabek D, van Haperen R, Townend S, van Kuppeveld FJM, Grosveld F, Ranson NA, Snijder J, de Groot RJ, Hurdiss DL, Bosch BJ. Antigenic structure of the human coronavirus OC43 spike reveals exposed and occluded neutralizing epitopes. Nat Commun 2022; 13:2921. [PMID: 35614127 PMCID: PMC9132891 DOI: 10.1038/s41467-022-30658-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/09/2022] [Indexed: 12/14/2022] Open
Abstract
Human coronavirus OC43 is a globally circulating common cold virus sustained by recurrent reinfections. How it persists in the population and defies existing herd immunity is unknown. Here we focus on viral glycoprotein S, the target for neutralizing antibodies, and provide an in-depth analysis of its antigenic structure. Neutralizing antibodies are directed to the sialoglycan-receptor binding site in S1A domain, but, remarkably, also to S1B. The latter block infection yet do not prevent sialoglycan binding. While two distinct neutralizing S1B epitopes are readily accessible in the prefusion S trimer, other sites are occluded such that their accessibility must be subject to conformational changes in S during cell-entry. While non-neutralizing antibodies were broadly reactive against a collection of natural OC43 variants, neutralizing antibodies generally displayed restricted binding breadth. Our data provide a structure-based understanding of protective immunity and adaptive evolution for this endemic coronavirus which emerged in humans long before SARS-CoV-2. Human coronavirus OC43 causes respiratory disease and is maintained in the human population through recurring infections. Here, by extensive structural analyses, the authors provide insights into the binding sites and breadth of neutralizing antibodies against this endemic coronavirus.
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Affiliation(s)
- Chunyan Wang
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Emma L Hesketh
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Tatiana M Shamorkina
- Biomolecular Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, P.R. China
| | - Peter J Franken
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Sarah Townend
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, The Netherlands.,Harbour BioMed, Rotterdam, The Netherlands
| | - Neil A Ranson
- Astbury Centre Structural Molecular Biology, School Molecular and Cellular Biology, Faculty Biological Sciences, University of Leeds, Leeds, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry & Proteomics, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Raoul J de Groot
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
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Known Cellular and Receptor Interactions of Animal and Human Coronaviruses: A Review. Viruses 2022; 14:v14020351. [PMID: 35215937 PMCID: PMC8878323 DOI: 10.3390/v14020351] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/12/2022] Open
Abstract
This article aims to review all currently known interactions between animal and human coronaviruses and their cellular receptors. Over the past 20 years, three novel coronaviruses have emerged that have caused severe disease in humans, including SARS-CoV-2 (severe acute respiratory syndrome virus 2); therefore, a deeper understanding of coronavirus host-cell interactions is essential. Receptor-binding is the first stage in coronavirus entry prior to replication and can be altered by minor changes within the spike protein-the coronavirus surface glycoprotein responsible for the recognition of cell-surface receptors. The recognition of receptors by coronaviruses is also a major determinant in infection, tropism, and pathogenesis and acts as a key target for host-immune surveillance and other potential intervention strategies. We aim to highlight the need for a continued in-depth understanding of this subject area following on from the SARS-CoV-2 pandemic, with the possibility for more zoonotic transmission events. We also acknowledge the need for more targeted research towards glycan-coronavirus interactions as zoonotic spillover events from animals to humans, following an alteration in glycan-binding capability, have been well-documented for other viruses such as Influenza A.
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11
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Abstract
Compared with other SARS-related coronaviruses (SARSr-CoVs), SARS-CoV-2 possesses a unique furin cleavage site (FCS) in its spike. This has stimulated discussion pertaining to the origin of SARS-CoV-2 because the FCS has been observed to be under strong selective pressure in humans and confers the enhanced ability to infect some cell types and induce cell-cell fusion. Furthermore, scientists have demonstrated interest in studying novel cleavage sites by introducing them into SARSr-CoVs. We review what is known about the SARS-CoV-2 FCS in the context of its pathogenesis, origin, and how future wildlife coronavirus sampling may alter the interpretation of existing data.
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Affiliation(s)
- Yujia Alina Chan
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Shing Hei Zhan
- Department of Zoology & Biodiversity Research Centre, University of British Columbia, Vancouver, BC, Canada
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12
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Sarker MT, Hasan AQF, Rafi MO, Hossain MJ, El-Mageed HRA, Elsapagh RM, Capasso R, Emran TB. A Comprehensive Overview of the Newly Emerged COVID-19 Pandemic: Features, Origin, Genomics, Epidemiology, Treatment, and Prevention. BIOLOGICS 2021; 1:357-383. [DOI: 10.3390/biologics1030021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
The coronavirus disease 2019 (COVID-19), a life-threatening pandemic caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has resulted in massive destruction and is still continuously adding to its death toll. The advent of this global outbreak has not yet been confirmed; however, investigation for suitable prophylaxis against this lethal virus is being carried out by experts all around the globe. The SARS-CoV-2 belongs to the Coronaviridae superfamily, like the other previously occurring human coronavirus variants. To better understand a new virus variant, such as the SARS-CoV-2 delta variant, it is vital to investigate previous virus strains, including their genomic composition and functionality. Our study aimed at addressing the basic overview of the virus’ profile that may provide the scientific community with evidence-based insights into COVID-19. Therefore, this study accomplished a comprehensive literature review that includes the virus’ origin, classification, structure, life cycle, genome, mutation, epidemiology, and subsequent essential factors associated with host–virus interaction. Moreover, we summarized the considerable diagnostic measures, treatment options, including multiple therapeutic approaches, and prevention, as well as future directions that may reduce the impact and misery caused by this devastating pandemic. The observations and data provided here have been screened and accumulated through extensive literature study, hence this study will help the scientific community properly understand this new virus and provide further leads for therapeutic interventions.
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13
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Parkhe P, Verma S. Evolution, Interspecies Transmission, and Zoonotic Significance of Animal Coronaviruses. Front Vet Sci 2021; 8:719834. [PMID: 34738021 PMCID: PMC8560429 DOI: 10.3389/fvets.2021.719834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/07/2021] [Indexed: 12/18/2022] Open
Abstract
Coronaviruses are single-stranded RNA viruses that affect humans and a wide variety of animal species, including livestock, wild animals, birds, and pets. These viruses have an affinity for different tissues, such as those of the respiratory and gastrointestinal tract of most mammals and birds and the hepatic and nervous tissues of rodents and porcine. As coronaviruses target different host cell receptors and show divergence in the sequences and motifs of their structural and accessory proteins, they are classified into groups, which may explain the evolutionary relationship between them. The interspecies transmission, zoonotic potential, and ability to mutate at a higher rate and emerge into variants of concern highlight their importance in the medical and veterinary fields. The contribution of various factors that result in their evolution will provide better insight and may help to understand the complexity of coronaviruses in the face of pandemics. In this review, important aspects of coronaviruses infecting livestock, birds, and pets, in particular, their structure and genome organization having a bearing on evolutionary and zoonotic outcomes, have been discussed.
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Affiliation(s)
| | - Subhash Verma
- Department of Veterinary Microbiology, DGCN College of Veterinary and Animal Sciences, Chaudhary Sarwan Kumar Himachal Pradesh Krishi Vishvavidyalaya, Palampur, India
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14
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Genomic evolution of the human and animal coronavirus diseases. Mol Biol Rep 2021; 48:6645-6653. [PMID: 34383242 PMCID: PMC8358252 DOI: 10.1007/s11033-021-06632-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 08/05/2021] [Indexed: 01/08/2023]
Abstract
Different coronaviruses have emerged due to their ability to infect, mutate and recombine multiple species and cell types, suggesting that these viruses will carry on to evolve and origin both veterinary and human diseases. So far, more than fifteen coronavirus-related diseases have been described in animals and seven in humans. Of which recently, a novel human betacoronavirus designated by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), an emerging zoonotic coronavirus is the causative agent of the coronavirus disease 2019. This virus emerged in China and spread rapidly worldwide. At the end of January 2020, the WHO declared the pandemic as a public health emergency of international concern. In this pandemic, the SARS-CoV-2 virus has infected more than 198 million people, with 4.2 million deaths worldwide (as of 2 August 2021). In the past two decades, this is the third betacoronavirus that has crossed the interspecies barrier from animals to infect humans and other animal species. The diseases caused mainly severe respiratory infections. The aim of this review is to summarize and provide an overview of the coronaviruses that can affect animals and humans and the diseases that ensue, as well as, its genomic relationship.
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15
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Benzigar MR, Bhattacharjee R, Baharfar M, Liu G. Current methods for diagnosis of human coronaviruses: pros and cons. Anal Bioanal Chem 2021; 413:2311-2330. [PMID: 33219449 PMCID: PMC7679240 DOI: 10.1007/s00216-020-03046-0] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/14/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022]
Abstract
The current global fight against coronavirus disease (COVID-19) to flatten the transmission curve is put forth by the World Health Organization (WHO) as there is no immediate diagnosis or cure for COVID-19 so far. In order to stop the spread, researchers worldwide are working around the clock aiming to develop reliable tools for early diagnosis of severe acute respiratory syndrome (SARS-CoV-2) understanding the infection path and mechanisms. Currently, nucleic acid-based molecular diagnosis (real-time reverse transcription polymerase chain reaction (RT-PCR) test) is considered the gold standard for early diagnosis of SARS-CoV-2. Antibody-based serology detection is ineffective for the purpose of early diagnosis, but a potential tool for serosurveys, providing people with immune certificates for clearance from COVID-19 infection. Meanwhile, there are various blooming methods developed these days. In this review, we summarise different types of coronavirus discovered which can be transmitted between human beings. Methods used for diagnosis of the discovered human coronavirus (SARS, MERS, COVID-19) including nucleic acid detection, gene sequencing, antibody detection, antigen detection, and clinical diagnosis are presented. Their merits, demerits and prospects are discussed which can help the researchers to develop new generation of advanced diagnostic tools for accurate and effective control of human coronavirus transmission in the communities and hospitals.
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Affiliation(s)
- Mercy R Benzigar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Ripon Bhattacharjee
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Mahroo Baharfar
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia
| | - Guozhen Liu
- Graduate School of Biomedical Engineering, University of New South Wales, Sydney, NSW, 2052, Australia.
- Australian Centre for NanoMedicine, University of New South Wales, Sydney, NSW, 2052, Australia.
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16
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El-Sayed A, Kamel M. Coronaviruses in humans and animals: the role of bats in viral evolution. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:19589-19600. [PMID: 33655480 PMCID: PMC7924989 DOI: 10.1007/s11356-021-12553-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 01/14/2021] [Indexed: 04/15/2023]
Abstract
Bats act as a natural reservoir for many viruses, including coronaviruses, and have played a crucial epidemiological role in the emergence of many viral diseases. Coronaviruses have been known for 60 years. They are usually responsible for the induction of mild respiratory signs in humans. However, since 2002, the bat-borne virus started to induce fatal epidemics according to WHO reports. In this year, the first serious human coronavirus epidemic (severe acute respiratory syndrome; SARS) occurred (China, 8098 cases, 774 deaths [9.5% of the cases] in 17 countries). The case fatality was higher in elderly patients above 60 years and reached 50% of the cases. SARS epidemic was followed 10 years later by the emergence of the middle east respiratory syndrome (MERS) in Saudi Arabia (in 2012, 2260 cases, 803 deaths [35.5% of the cases] in 27 countries). Finally, in December 2019, a new epidemic in Wuhan, China, (corona virus disease 2019, COVID-19) emerged and could spread to 217 countries infecting more than 86,255,226 cases and killing 1,863,973 people by the end of 2020. There are many reasons why bats are ideal reservoir hosts for viral diseases such as the tolerance of their immune system to the invading viruses for several months. They can actively shed the viruses, although they develop no clinical signs (will be discussed in details later in the review). Bats were directly or indirectly involved in the three previous coronavirus epidemics. The indirect transmission takes place via intermediate hosts including civet cats for SARS and dromedary camels in the case of MERS. Although bats are believed to be the source of COVID-19 pandemic, direct pieces of evidence are still lacking. Therefore, coronaviruses' role in epidemics induction and the epidemiological role of bats are discussed. The current work also presents different evidence (phylogenetic data, animal experiments, bats artificial infection studies, and computerized models of SARS-CoV2 evolution) that underline the involvement of bats in the epidemiology of the pandemic.
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Affiliation(s)
- Amr El-Sayed
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt
| | - Mohamed Kamel
- Department of Medicine and Infectious Diseases, Faculty of Medicine and Infectious Diseases, Cairo University, Giza, 12211, Egypt.
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17
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Al-Tawfiq JA, Rabaan AA, Al-Omari A, Al Mutair A, Al-Qahtani M, Tirupathi R. Learning from SARS and MERS: COVID-19 reinfection where do we stand? Travel Med Infect Dis 2021; 41:102024. [PMID: 33741499 PMCID: PMC7962586 DOI: 10.1016/j.tmaid.2021.102024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 01/28/2023]
Affiliation(s)
- Jaffar A Al-Tawfiq
- Specialty Internal Medicine and Quality Department, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Division of Infectious Diseases, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, USA; Division of Infectious Diseases, Department of Medicine Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - Awad Al-Omari
- Research Center, Dr. Sulaiman Al Habib Medical Group, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Abbas Al Mutair
- Research Center, Almoosa Specialist Hospital, Al Hasa, Saudi Arabia; College of Nursing, prince Nora University, Riyadh, Saudi Arabia; School of Nursing, Wollongong University, Australia
| | - Manaf Al-Qahtani
- Bahrain National Taskforce to Combat COVID-19, Bahrain Defense Force Hospital, Bahrain
| | - Raghavendra Tirupathi
- Penn State University School of Medicine, Hershey, PA, USA; Wellspan Chambersburg and Waynesboro (Pa.) Hospitals, Chambersburg, PA, USA
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18
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Ng KT, Mohd-Ismail NK, Tan YJ. Spike S2 Subunit: The Dark Horse in the Race for Prophylactic and Therapeutic Interventions against SARS-CoV-2. Vaccines (Basel) 2021; 9:178. [PMID: 33672450 PMCID: PMC7923282 DOI: 10.3390/vaccines9020178] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
In the midst of the unceasing COVID-19 pandemic, the identification of immunogenic epitopes in the SARS-CoV-2 spike (S) glycoprotein plays a vital role in the advancement and development of intervention strategies. S is expressed on the exterior of the SARS-CoV-2 virion and contains two subunits, namely the N-terminal S1 and C-terminal S2. It is the key element for mediating viral entry as well as a crucial antigenic determinant capable of stimulating protective immune response through elicitation of anti-SARS-CoV-2 antibodies and activation of CD4+ and CD8+ cells in COVID-19 patients. Given that S2 is highly conserved in comparison to the S1, here, we provide a review of the latest findings on the SARS-CoV-2 S2 subunit and further discuss its potential as an attractive and promising target for the development of prophylactic vaccines and therapeutic agents against COVID-19.
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Affiliation(s)
- Kim Tien Ng
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Nur Khairiah Mohd-Ismail
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yee-Joo Tan
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
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19
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Sofi MS, Hamid A, Bhat SU. SARS-CoV-2: A critical review of its history, pathogenesis, transmission, diagnosis and treatment. BIOSAFETY AND HEALTH 2020; 2:217-225. [PMID: 33196035 PMCID: PMC7648888 DOI: 10.1016/j.bsheal.2020.11.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 01/08/2023] Open
Abstract
The outbreak of the deadly virus (novel coronavirus or Severe Acute Respiratory Syndrome Coronavirus-2) that emerged in December 2019, remained a controversial subject of intense speculations regarding its origin, became a worldwide health problem resulting in serious coronavirus disease 2019 (acronym COVID-19). The concern regarding this new viral strain "Severe Acute Respiratory Syndrome Coronavirus-2" (acronym SARS-CoV-2) and diseases it causes (COVID-19) is well deserved at all levels. The incidence of COVID-19 infection and infectious patients are increasing at a high rate. Coronaviruses (CoVs), enclosed positive-sense RNA viruses, are distinguished by club-like spikes extending from their surface, an exceptionally large genome of RNA, and a special mechanism for replication. Coronaviruses are associated with a broad variety of human and other animal diseases spanning from enteritis in cattle and pigs and upper chicken respiratory disease to extremely lethal human respiratory infections. With World Health Organization (WHO) declaring COVID-19 as pandemic, we deemed it necessary to provide a detailed review of coronaviruses discussing their history, current situation, coronavirus classification, pathogenesis, structure, mode of action, diagnosis and treatment, the effect of environmental factors, risk reduction and guidelines to understand the virus and develop ways to control it.
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Affiliation(s)
| | | | - Sami Ullah Bhat
- Corresponding author: Department of Environmental Science, School of Earth and Environmental Science, University of Kashmir, 190006, India
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20
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Cimolai N. Complicating Infections Associated with Common Endemic Human Respiratory Coronaviruses. Health Secur 2020; 19:195-208. [PMID: 33186086 DOI: 10.1089/hs.2020.0067] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Coronaviruses OC43, 229E, NL63, and HKU1 are endemic human respiratory coronaviruses that typically cause mild to moderate upper respiratory infections, similar to the common cold. They also may cause simple and complicated lower respiratory infections, otitis media, asthma exacerbations, gastroenteritis, and a few systemic complications. These viruses are usually seasonal (with winter dominance) and affect nearly all age groups. The seasonal and annual variation in virus prevalence has implications for understanding the concept of acquired immunity and its persistence or diminution. Coronaviruses generally have outbreak potential in susceptible populations of any age, particularly in patients with comorbidities, who tend to have increased clinical disease. These 4 coronaviruses are often found in the context of what appears to be coinfection with other pathogens, but especially other viruses. If coronaviruses are not specifically tested for, the sole detection of a viral copathogen would suggest the pathogen is the causative agent, when a coronavirus may be culpable, or both. The detection of these viruses in circumstances where respiratory viruses are generally sought in clinical samples is, therefore, justified. These pathogens can be chronically shed from the respiratory tract, which is more likely to occur among immunocompromised and complicated patients. These viruses share the potential for genetic drift. The genome is among the largest of RNA viruses, and the capability of these viruses to further change is likely underestimated. Given the potential disease among humans, it is justified to search for effective antiviral chemotherapy for these viruses and to consider uses in niche situations should effective therapy be defined. Whereas SARS-CoV-2 may follow the epidemiological pattern of SARS-CoV and extinguish slowly over time, there is yet concern that SARS-CoV-2 may establish itself as an endemic human respiratory coronavirus similar to OC43, 2299E, NL63, and HKU1. Until sufficient data are acquired to better understand the potential of SARS-CoV-2, continued work on antiviral therapy and vaccination is imperative.
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Affiliation(s)
- Nevio Cimolai
- Nevio Cimolai, MD, FRCPC, is a Professor, Department of Pathology and Laboratory Medicine, Faculty of Medicine, University of British Columbia; he is also Medical Staff, Pathology and Laboratory Medicine, Children's and Women's Health Centre of British Columbia; both in Vancouver, Canada
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21
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Ling J, Hickman RA, Li J, Lu X, Lindahl JF, Lundkvist Å, Järhult JD. Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic. Viruses 2020; 12:E1026. [PMID: 32937868 PMCID: PMC7551444 DOI: 10.3390/v12091026] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. METHODS We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. RESULTS We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10-3 substitutions per year. CONCLUSIONS Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.
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Affiliation(s)
- Jiaxin Ling
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Rachel A. Hickman
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Jinlin Li
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- Department of Cell and Molecular Biology, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | - Xi Lu
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China;
| | - Johanna F. Lindahl
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
- International Livestock Research Institute, Nairobi 00100, Kenya
- Swedish University of Agricultural Research, SE-750 07 Uppsala, Sweden
| | - Åke Lundkvist
- Department of Medical Biochemistry and Microbiology, Zoonosis Science Center, University of Uppsala, SE-751 23 Uppsala, Sweden; (J.L.); (J.F.L.); (Å.L.)
| | - Josef D. Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, SE-751 23 Uppsala, Sweden;
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22
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Wang Y, Grunewald M, Perlman S. Coronaviruses: An Updated Overview of Their Replication and Pathogenesis. Methods Mol Biol 2020; 2203:1-29. [PMID: 32833200 DOI: 10.1007/978-1-0716-0900-2_1] [Citation(s) in RCA: 113] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. CoVs cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs, and upper respiratory tract and kidney disease in chickens to lethal human respiratory infections. Most recently, the novel coronavirus, SARS-CoV-2, which was first identified in Wuhan, China in December 2019, is the cause of a catastrophic pandemic, COVID-19, with more than 8 million infections diagnosed worldwide by mid-June 2020. Here we provide a brief introduction to CoVs discussing their replication, pathogenicity, and current prevention and treatment strategies. We will also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV), which are relevant for understanding COVID-19.
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Affiliation(s)
- Yuhang Wang
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Matthew Grunewald
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA, USA.
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23
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043s] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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24
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020; 182:812-827.e19. [PMID: 32697968 PMCID: PMC7332439 DOI: 10.1016/j.cell.2020.06.043] [Citation(s) in RCA: 2795] [Impact Index Per Article: 698.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 06/10/2020] [Accepted: 06/26/2020] [Indexed: 02/08/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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25
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Korber B, Fischer WM, Gnanakaran S, Yoon H, Theiler J, Abfalterer W, Hengartner N, Giorgi EE, Bhattacharya T, Foley B, Hastie KM, Parker MD, Partridge DG, Evans CM, Freeman TM, de Silva TI, McDanal C, Perez LG, Tang H, Moon-Walker A, Whelan SP, LaBranche CC, Saphire EO, Montefiori DC. Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus. Cell 2020. [PMID: 32697968 DOI: 10.1016/j.cell.2020.06.043%0asummary] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic. Dynamic tracking of variant frequencies revealed a recurrent pattern of G614 increase at multiple geographic levels: national, regional, and municipal. The shift occurred even in local epidemics where the original D614 form was well established prior to introduction of the G614 variant. The consistency of this pattern was highly statistically significant, suggesting that the G614 variant may have a fitness advantage. We found that the G614 variant grows to a higher titer as pseudotyped virions. In infected individuals, G614 is associated with lower RT-PCR cycle thresholds, suggestive of higher upper respiratory tract viral loads, but not with increased disease severity. These findings illuminate changes important for a mechanistic understanding of the virus and support continuing surveillance of Spike mutations to aid with development of immunological interventions.
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Affiliation(s)
- Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; New Mexico Consortium, Los Alamos, NM 87545, USA.
| | - Will M Fischer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Hyejin Yoon
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - James Theiler
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Werner Abfalterer
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Nick Hengartner
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Elena E Giorgi
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Tanmoy Bhattacharya
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Brian Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Matthew D Parker
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - David G Partridge
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Cariad M Evans
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK
| | - Timothy M Freeman
- Sheffield Biomedical Research Centre & Sheffield Bioinformatics Core, University of Sheffield, Sheffield S10 2HQ, UK
| | - Thushan I de Silva
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield S10 2JF, UK; Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield S10 2RX, UK
| | - Charlene McDanal
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Lautaro G Perez
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Haili Tang
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | - Alex Moon-Walker
- La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Program in Virology, Harvard University, Boston, MA 02115, USA; Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Sean P Whelan
- Department of Molecular Microbiology, Washington University in Saint Louis, St. Louis, MO 63130, USA
| | - Celia C LaBranche
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
| | | | - David C Montefiori
- Duke Human Vaccine Institute & Department of Surgery, Durham, NC 27710, USA
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Kellam P, Barclay W. The dynamics of humoral immune responses following SARS-CoV-2 infection and the potential for reinfection. J Gen Virol 2020; 101:791-797. [PMID: 32430094 PMCID: PMC7641391 DOI: 10.1099/jgv.0.001439] [Citation(s) in RCA: 248] [Impact Index Per Article: 62.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 05/04/2020] [Indexed: 12/12/2022] Open
Abstract
SARS-CoV-2 is a novel coronavirus that is the causative agent of coronavirus infectious disease 2019 (COVID-19). As of 17 April 2020, it has infected 2 114 269 people, resulting in 145 144 deaths. The timing, magnitude and longevity of humoral immunity is not yet understood for SARS-CoV-2. Nevertheless, understanding this is urgently required to inform the likely future dynamics of the pandemic, to guide strategies to allow relaxation of social distancing measures and to understand how to deploy limiting vaccine doses when they become available to achieve maximum impact. SARS-CoV-2 is the seventh human coronavirus to be described. Four human coronaviruses circulate seasonally and cause common colds. Two other coronaviruses, SARS and MERS, have crossed from animal sources into humans but have not become endemic. Here we review what is known about the human humoral immune response to epidemic SARS CoV and MERS CoV and to the seasonal, endemic coronaviruses. Then we summarize recent, mostly non-peer reviewed, studies into SARS-CoV-2 serology and reinfection in humans and non-human primates and summarize current pressing research needs.
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Affiliation(s)
- Paul Kellam
- Department of Infectious Diseases, Faulty of Medicine, Imperial College London, London, W2 1NY, UK
- Kymab Ltd, The Bennet Building (B930), Babraham Research Campus, Cambridge, CB22 3AT, UK
| | - Wendy Barclay
- Department of Infectious Diseases, Faulty of Medicine, Imperial College London, London, W2 1NY, UK
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Leao JC, Gusmao TPDL, Zarzar AM, Leao Filho JC, Barkokebas Santos de Faria A, Morais Silva IH, Gueiros LAM, Robinson NA, Porter S, Carvalho ADAT. Coronaviridae-Old friends, new enemy! Oral Dis 2020; 28 Suppl 1:858-866. [PMID: 32475006 PMCID: PMC7300831 DOI: 10.1111/odi.13447] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 05/09/2020] [Accepted: 05/14/2020] [Indexed: 01/08/2023]
Abstract
Coronaviridae is a family of single‐stranded positive enveloped RNA viruses. This article aimed to review the history of these viruses in the last 60 years since their discovery to understand what lessons can be learned from the past. A review of the PubMed database was carried out, describing taxonomy, classification, virology, genetic recombination, host adaptation, and main symptoms related to each type of virus. SARS‐CoV‐2 is responsible for the ongoing global pandemic, and SARS‐CoV and MERS‐CoV were responsible for causing severe respiratory illness and regional epidemics in the past while the four other strains of CoVs (229‐E OC43, NL63, and HKU1) circulate worldwide and normally only cause mild upper respiratory tract infections. Given the enormous diversity of coronavirus viruses in wildlife and their continuous evolution and adaptation to humans, future outbreaks would undoubtedly occur. Restricting or banning all trade in wild animals in wet markets would be a necessary measure to reduce future zoonotic infections.
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Affiliation(s)
- Jair Carneiro Leao
- Departamento de Clínica e Odontologia Preventiva, Universidade Federal de Pernambuco, Recife, Brazil
| | | | - Adriana Machado Zarzar
- Departamento de Clínica e Odontologia Preventiva, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | | | - Narendran Andrew Robinson
- Discipline of Oral and Maxillofacial Surgery, Faculty of Dentistry, National University of Singapore, Singapore City, Singapore
| | - Stephen Porter
- Maxillofacial Medicine & Surgery Department, Eastman Dental Institute, University College London, London, UK
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28
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Global Transmission, Spatial Segregation, and Recombination Determine the Long-Term Evolution and Epidemiology of Bovine Coronaviruses. Viruses 2020; 12:v12050534. [PMID: 32414076 PMCID: PMC7290379 DOI: 10.3390/v12050534] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/10/2020] [Accepted: 05/11/2020] [Indexed: 01/15/2023] Open
Abstract
Bovine coronavirus (BCoV) is widespread in cattle and wild ruminant populations throughout the world. The virus causes neonatal calf diarrhea and winter dysentery in adult cattle, as well as upper and lower respiratory tract infection in young cattle. We isolated and deep sequenced whole genomes of BCoV from calves with respiratory distress in the south–west of France and conducted a comparative genome analysis using globally collected BCoV sequences to provide insights into the genomic characteristics, evolutionary origins, and global diversity of BCoV. Molecular clock analyses allowed us to estimate that the BCoV ancestor emerged in the 1940s, and that two geographically distinct lineages diverged from the 1960s–1970s. A recombination event in the spike gene (breakpoint at nt 1100) may be at the origin of the genetic divergence sixty years ago. Little evidence of genetic mixing between the spatially segregated lineages was found, suggesting that BCoV genetic diversity is a result of a global transmission pathway that occurred during the last century. However, we found variation in evolution rates between the European and non-European lineages indicating differences in virus ecology.
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29
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Lundstrom K. Coronavirus Pandemic-Therapy and Vaccines. Biomedicines 2020; 8:E109. [PMID: 32375268 PMCID: PMC7277397 DOI: 10.3390/biomedicines8050109] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/13/2022] Open
Abstract
The current coronavirus COVID-19 pandemic, which originated in Wuhan, China, has raised significant social, psychological and economic concerns in addition to direct medical issues. The rapid spread of severe acute respiratory syndrome-coronavirus (SARS-CoV)-2 to almost every country on the globe and the failure to contain the infections have contributed to fear and panic worldwide. The lack of available and efficient antiviral drugs or vaccines has further worsened the situation. For these reasons, it cannot be overstated that an accelerated effort for the development of novel drugs and vaccines is needed. In this context, novel approaches in both gene therapy and vaccine development are essential. Previous experience from SARS- and MERS-coronavirus vaccine and drug development projects have targeted glycoprotein epitopes, monoclonal antibodies, angiotensin receptor blockers and gene silencing technologies, which may be useful for COVID-19 too. Moreover, existing antivirals used for other types of viral infections have been considered as urgent action is necessary. This review aims at providing a background of coronavirus genetics and biology, examples of therapeutic and vaccine strategies taken and potential innovative novel approaches in progress.
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30
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Zhu Y, Li C, Chen L, Xu B, Zhou Y, Cao L, Shang Y, Fu Z, Chen A, Deng L, Bao Y, Sun Y, Ning L, Liu C, Yin J, Xie Z, Shen K. A novel human coronavirus OC43 genotype detected in mainland China. Emerg Microbes Infect 2018; 7:173. [PMID: 30377292 PMCID: PMC6207742 DOI: 10.1038/s41426-018-0171-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Accepted: 09/02/2018] [Indexed: 01/27/2023]
Affiliation(s)
- Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Changchong Li
- The 2nd Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Li Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Baoping Xu
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yunlian Zhou
- The Children's Hospital-Zhejiang University School of Medicine, Hangzhou, China
| | - Ling Cao
- Children's Hospital Capital Institute of Pediatrics, Beijing, China
| | - Yunxiao Shang
- Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhou Fu
- Children's Hospital of Chongqing Medical University, Chongqing, China
| | - Aihuan Chen
- The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Li Deng
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yixiao Bao
- Xin Hua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yun Sun
- Yinchuan Women and Children Healthcare Hospital, Yinchuan, China
| | - Limin Ning
- Children's hospital of Changchun, Changchun, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Ju Yin
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Kunling Shen
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
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Beidas M, Chehadeh W. Effect of Human Coronavirus OC43 Structural and Accessory Proteins on the Transcriptional Activation of Antiviral Response Elements. Intervirology 2018; 61:30-35. [PMID: 30041172 PMCID: PMC7179558 DOI: 10.1159/000490566] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 06/03/2018] [Indexed: 12/25/2022] Open
Abstract
Objectives The molecular mechanisms underlying the pathogenesis of human coronavirus OC43 (HCoV-OC43) infection are poorly understood. In this study, we investigated the ability of HCoV-OC43 to antagonize the transcriptional activation of antiviral response elements. Methods HCoV-OC43 structural (membrane M and nucleocapsid N) and accessory proteins (ns2a and ns5a) were expressed individually in human embryonic kidney 293 (HEK-293) cells. The transcriptional activation of antiviral response elements was assessed by measuring the levels of firefly luciferase expressed under the control of interferon (IFN)-stimulated response element (ISRE), IFN-β promoter, or nuclear factor kappa B response element (NF-κB-RE). The antiviral gene expression profile in HEK-293 cells was determined by PCR array. Results The transcriptional activity of ISRE, IFN-β promoter, and NF-κB-RE was significantly reduced in the presence of HCoV-OC43 ns2a, ns5a, M, or N protein, following the challenge of cells with Sendai virus, IFN-α or tumor necrosis factor-α. The expression of antiviral genes involved in the type I IFN and NF-κB signaling pathways was also downregulated in the presence of HCoV-OC43 structural or accessory proteins. Conclusion Both structural and accessory HCoV-OC43 proteins are able to inhibit antiviral response elements in HEK-293 cells, and to block the activation of different antiviral signaling pathways.
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Affiliation(s)
| | - Wassim Chehadeh
- *Dr. Wassim Chehadeh, Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, Safat 13310 (Kuwait), E-Mail
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Brandão PE. Could human coronavirus OC43 have co-evolved with early humans? Genet Mol Biol 2018; 41:692-698. [PMID: 30004106 PMCID: PMC6136381 DOI: 10.1590/1678-4685-gmb-2017-0192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Accepted: 01/05/2018] [Indexed: 12/24/2022] Open
Abstract
This paper reports on an investigation of the role of codon usage evolution on the suggested bovine-to-human spillover of Bovine coronavirus (BCoV), an enteric/respiratory virus of cattle, resulting in the emergence of the exclusively respiratory Human coronavirus OC43 (HCoV-OC43). Analyses based on full genomes of BCoV and HCoV-OC43 and on both human and bovine mRNAs sequences of cholecystokinin (CCK) and surfactant protein 1 A (SFTP1-A), representing the enteric and respiratory tract codon usage, respectively, have shown natural selection leading to optimization or deoptimization of viral codon usage to the human enteric and respiratory tracts depending on the virus genes under consideration. A higher correlation was found for the nucleotide distance at the 3rd nucleotide position of codons and codon usage optimization to the human respiratory tract when BCoV and HCoV-OC43 were compared. An MCC tree based on relative synonymous codon usage (RSCU) data integrating data from both viruses and hosts into a same analysis indicated three putative host/virus contact dates ranging from 1.54E8 to 2.44E5 years ago, suggesting that an ancestor coronavirus might have followed human evolution.
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Affiliation(s)
- Paulo Eduardo Brandão
- Departmento de Medicina Veterinaria Preventiva e Saúde Animal, Faculdade de Medicina Veterinária e Zootecnia, Universidade de São Paulo, São Paulo, SP, Brazil
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Beidas M, Chehadeh W. PCR array profiling of antiviral genes in human embryonic kidney cells expressing human coronavirus OC43 structural and accessory proteins. Arch Virol 2018; 163:2065-2072. [PMID: 29619598 PMCID: PMC7086905 DOI: 10.1007/s00705-018-3832-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Accepted: 03/22/2018] [Indexed: 10/26/2022]
Abstract
Human coronavirus OC43 (HCoV-OC43) is a respiratory virus that usually causes a common cold. However, it has the potential to cause severe infection in young children and immunocompromised adults. Both SARS-CoV and MERS-CoV were shown to express proteins with the potential to evade early innate immune responses. However, the ability of HCoV-OC43 to antagonise the intracellular antiviral defences has not yet been investigated. The potential role of the HCoV-OC43 structural (M and N) and accessory proteins (ns2a and ns5a) in the alteration of antiviral gene expression was investigated in this study. HCoV-OC43M, N, ns2a and ns5a proteins were expressed in human embryonic kidney 293 (HEK-293) cells before challenge with Sendai virus. The Human Antiviral Response PCR array was used to profile the antiviral gene expression in HEK-293 cells. Over 30 genes were downregulated in the presence of one of the HCoV-OC43 proteins, e.g. genes representing mitogen-activated protein kinases, toll-like receptors, interferons, interleukins, and signaling transduction proteins. Our findings suggest that similarly to SARS-CoV and MERS-CoV, HCoV-OC43 has the ability to downregulate the transcription of genes critical for the activation of different antiviral signaling pathways. Further studies are needed to confirm the role of HCoV-OC43 structural and accessory proteins in antagonising antiviral gene expression.
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Affiliation(s)
- Meshal Beidas
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, 13310, Safat, Kuwait
| | - Wassim Chehadeh
- Department of Microbiology, Faculty of Medicine, Kuwait University, PO Box 24923, 13310, Safat, Kuwait.
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Liu P, Shi L, Zhang W, He J, Liu C, Zhao C, Kong SK, Loo JFC, Gu D, Hu L. Prevalence and genetic diversity analysis of human coronaviruses among cross-border children. Virol J 2017; 14:230. [PMID: 29166910 PMCID: PMC5700739 DOI: 10.1186/s12985-017-0896-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Accepted: 11/15/2017] [Indexed: 12/16/2022] Open
Abstract
Background More than a decade after the outbreak of human coronaviruses (HCoVs) SARS in Guangdong province and Hong Kong SAR of China in 2002, there is still no reoccurrence, but the evolution and recombination of the coronaviruses in this region are still unknown. Therefore, surveillance on the prevalence and the virus variation of HCoVs circulation in this region is conducted. Methods A total of 3298 nasopharyngeal swabs samples were collected from cross-border children (<6 years, crossing border between Southern China and Hong Kong SAR) showing symptoms of respiratory tract infection, such as fever (body temperature > 37.5 °C), from 2014 May to 2015 Dec. Viral nucleic acids were analyzed and sequenced to study the prevalence and genetic diversity of the four human coronaviruses. The statistical significance of the data was evaluated with Fisher chi-square test. Results 78 (2.37%; 95%CI 1.8-2.8%) out of 3298 nasopharyngeal swabs specimens were found to be positive for OC43 (36;1.09%), HKU1 (34; 1.03%), NL63 (6; 0.18%) and 229E (2;0.01%). None of SARS or MERS was detected. The HCoVs predominant circulating season was in transition of winter to spring, especially January and February and NL63 detected only in summer and fall. Complex population with an abundant genetic diversity of coronaviruses was circulating and they shared homology with the published strains (99-100%). Besides, phylogenetic evolutionary analysis indicated that OC43 coronaviruses were clustered into three clades (B,D,E), HKU1 clustered into two clades(A,B) and NL63 clustered into two clades(A,B). Moreover, several novel mutations including nucleotides substitution and the insertion of spike of the glycoprotein on the viral surface were discovered. Conclusions The detection rate and epidemic trend of coronaviruses were stable and no obvious fluctuations were found. The detected coronaviruses shared a conserved gene sequences in S and RdRp. However, mutants of the epidemic strains were detected, suggesting continuous monitoring of the human coronaviruses is in need among cross-border children, who are more likely to get infected and transmit the viruses across the border easily, in addition to the general public.
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Affiliation(s)
- Peilin Liu
- Department of Health Inspection and Quarantine, School of Public Health, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.,Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Lei Shi
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Wei Zhang
- Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, People's Republic of China
| | - Jianan He
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Chunxiao Liu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Chunzhong Zhao
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China
| | - Siu Kai Kong
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Jacky Fong Chuen Loo
- Biochemistry Programme, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China. .,Department of Biomedical Engineering, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR, China.
| | - Dayong Gu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. .,Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China.
| | - Longfei Hu
- Central Laboratory of Health quarantine, Shenzhen International Travel Health Care Center and Shenzhen Academy of Inspection and Quarantine, Shenzhen Entry-exit Inspection and Quarantine Bureau, Shenzhen, 518033, People's Republic of China. .,Shenzhen Academy of Inspection and Quarantine, Shenzhen, 518010, People's Republic of China.
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Gorse GJ, Patel GB, Fan X. Interpatient mutational spectrum of human coronavirus-OC43 revealed by illumina sequencing. J Med Virol 2017; 89:1330-1338. [PMID: 28191658 PMCID: PMC7166611 DOI: 10.1002/jmv.24780] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 01/03/2017] [Indexed: 12/30/2022]
Abstract
Human coronaviruses (HCoV) are RNA viruses that cause respiratory tract infections with viral replication of limited duration. The host and viral population heterogeneity could influence clinical phenotypes. Employing long RT‐PCR with Illumina sequencing, we quantified the gene mutation load at 0.5% mutation frequency for the 4529 bp‐domain spanning the Spike gene (4086 bp) of HCoV‐OC43 in four upper respiratory clinical specimens obtained during acute illness. There were a total of 121 mutations for all four HCoV samples with the average number of mutations at 30.3 ± 10.2, which is significantly higher than that expected from the Illumina sequencing error rate. There were two mutation peaks, one at the 5′ end and the other near position 1 550 in the S1 subunit. Two coronavirus samples were genotype B and two were genotype D, clustering with HCoV‐OC43 strain AY391777 in neighbor‐joining tree phylogenetic analysis. Nonsynonymous mutations were 76.1 ± 14% of mutation load. Although lower than other RNA viruses such as hepatitis C virus, HCoV‐OC43 did exhibit quasi‐species. The rate of nonsynonymous mutations was higher in the HCoV‐OC43 isolates than in hepatitis C (HCV) virus genotype 1a isolates analyzed for comparison in this study. These characteristics of HCoV‐OC43 may affect viral replication dynamics, receptor binding, antigenicity, evolution, transmission, and clinical illness.
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Affiliation(s)
- Geoffrey J Gorse
- VA St. Louis Health Care System, St. Louis, Missouri.,Division of Infectious Diseases, Allergy and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Gira B Patel
- VA St. Louis Health Care System, St. Louis, Missouri.,Division of Infectious Diseases, Allergy and Immunology, Saint Louis University School of Medicine, St. Louis, Missouri
| | - Xiaofeng Fan
- Division of Gastroenterology and Hepatology, Saint Louis University School of Medicine, St. Louis, Missouri
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36
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Identification and evolutionary dynamics of two novel human coronavirus OC43 genotypes associated with acute respiratory infections: phylogenetic, spatiotemporal and transmission network analyses. Emerg Microbes Infect 2017; 6:e3. [PMID: 28050020 PMCID: PMC5285497 DOI: 10.1038/emi.2016.132] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 11/18/2016] [Accepted: 11/21/2016] [Indexed: 02/05/2023]
Abstract
Human coronavirus OC43 (HCoV-OC43) is commonly associated with respiratory tract infections in humans, with five genetically distinct genotypes (A to E) described so far. In this study, we obtained the full-length genomes of HCoV-OC43 strains from two previously unrecognized lineages identified among patients presenting with severe upper respiratory tract symptoms in a cross-sectional molecular surveillance study in Kuala Lumpur, Malaysia, between 2012 and 2013. Phylogenetic, recombination and comparative genomic analyses revealed two distinct clusters diverging from a genotype D-like common ancestor through recombination with a putative genotype A-like lineage in the non-structural protein (nsp) 10 gene. Signature amino acid substitutions and a glycine residue insertion at the N-terminal domain of the S1 subunit of the spike gene, among others, exhibited further distinction in a recombination pattern, to which these clusters were classified as genotypes F and G. The phylogeographic mapping of the global spike gene indicated that the genetically similar HCoV-OC43 genotypes F and G strains were potentially circulating in China, Japan, Thailand and Europe as early as the late 2000s. The transmission network construction based on the TN93 pairwise genetic distance revealed the emergence and persistence of multiple sub-epidemic clusters of the highly prevalent genotype D and its descendant genotypes F and G, which contributed to the spread of HCoV-OC43 in the region. Finally, a more consistent nomenclature system for non-recombinant and recombinant HCoV-OC43 lineages is proposed, taking into account genetic recombination as an important feature in HCoV evolution and classification.
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Abstract
Human rhinovirus (HRV) and coronavirus (HCoV) infections are associated with both upper respiratory tract illness (“the common cold”) and lower respiratory tract illness (pneumonia). New species of HRVs and HCoVs have been diagnosed in the past decade. More sensitive diagnostic tests such as reverse transcription-polymerase chain reaction have expanded our understanding of the role these viruses play in both immunocompetent and immunosuppressed hosts. Recent identification of severe acute respiratory syndrome and Middle East respiratory syndrome viruses causing serious respiratory illnesses has led to renewed efforts for vaccine development. The role these viruses play in patients with chronic lung disease such as asthma makes the search for antiviral agents of increased importance.
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Affiliation(s)
- Stephen B Greenberg
- Department of Medicine, Ben Taub Hospital, Baylor College of Medicine, Houston, Texas
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Al-Khannaq MN, Ng KT, Oong XY, Pang YK, Takebe Y, Chook JB, Hanafi NS, Kamarulzaman A, Tee KK. Molecular epidemiology and evolutionary histories of human coronavirus OC43 and HKU1 among patients with upper respiratory tract infections in Kuala Lumpur, Malaysia. Virol J 2016; 13:33. [PMID: 26916286 PMCID: PMC4766700 DOI: 10.1186/s12985-016-0488-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/11/2016] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Despite the worldwide circulation of human coronavirus OC43 (HCoV-OC43) and HKU1 (HCoV-HKU1), data on their molecular epidemiology and evolutionary dynamics in the tropical Southeast Asia region is lacking. METHODS The study aimed to investigate the genetic diversity, temporal distribution, population history and clinical symptoms of betacoronavirus infections in Kuala Lumpur, Malaysia between 2012 and 2013. A total of 2,060 adults presented with acute respiratory symptoms were screened for the presence of betacoronaviruses using multiplex PCR. The spike glycoprotein, nucleocapsid and 1a genes were sequenced for phylogenetic reconstruction and Bayesian coalescent inference. RESULTS A total of 48/2060 (2.4 %) specimens were tested positive for HCoV-OC43 (1.3 %) and HCoV-HKU1 (1.1 %). Both HCoV-OC43 and HCoV-HKU1 were co-circulating throughout the year, with the lowest detection rates reported in the October-January period. Phylogenetic analysis of the spike gene showed that the majority of HCoV-OC43 isolates were grouped into two previously undefined genotypes, provisionally assigned as novel lineage 1 and novel lineage 2. Sign of natural recombination was observed in these potentially novel lineages. Location mapping showed that the novel lineage 1 is currently circulating in Malaysia, Thailand, Japan and China, while novel lineage 2 can be found in Malaysia and China. Molecular dating showed the origin of HCoV-OC43 around late 1950s, before it diverged into genotypes A (1960s), B (1990s), and other genotypes (2000s). Phylogenetic analysis revealed that 27.3 % of the HCoV-HKU1 strains belong to genotype A while 72.7 % belongs to genotype B. The tree root of HCoV-HKU1 was similar to that of HCoV-OC43, with the tMRCA of genotypes A and B estimated around the 1990s and 2000s, respectively. Correlation of HCoV-OC43 and HCoV-HKU1 with the severity of respiratory symptoms was not observed. CONCLUSIONS The present study reported the molecular complexity and evolutionary dynamics of human betacoronaviruses among adults with acute respiratory symptoms in a tropical country. Two novel HCoV-OC43 genetic lineages were identified, warranting further investigation on their genotypic and phenotypic characteristics.
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Affiliation(s)
| | - Kim Tien Ng
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Xiang Yong Oong
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yong Kek Pang
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Yutaka Takebe
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
- AIDS Research Center, National Institute of Infectious Diseases, Toyama, Shinjuku-ku, Tokyo, Japan.
- School of Medicine, Yokohama City University, Yokohama, Kanagawa, Japan.
| | - Jack Bee Chook
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Nik Sherina Hanafi
- Department of Primary Care Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Adeeba Kamarulzaman
- Department of Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Kok Keng Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
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Goffard A, Demanche C, Arthur L, Pinçon C, Michaux J, Dubuisson J. Alphacoronaviruses Detected in French Bats Are Phylogeographically Linked to Coronaviruses of European Bats. Viruses 2015; 7:6279-90. [PMID: 26633467 PMCID: PMC4690861 DOI: 10.3390/v7122937] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Revised: 11/17/2015] [Accepted: 11/23/2015] [Indexed: 12/14/2022] Open
Abstract
Bats are a reservoir for a diverse range of viruses, including coronaviruses (CoVs). To determine the presence of CoVs in French bats, fecal samples were collected between July and August of 2014 from four bat species in seven different locations around the city of Bourges in France. We present for the first time the presence of alpha-CoVs in French Pipistrellus pipistrellus bat species with an estimated prevalence of 4.2%. Based on the analysis of a fragment of the RNA-dependent RNA polymerase (RdRp) gene, phylogenetic analyses show that alpha-CoVs sequences detected in French bats are closely related to other European bat alpha-CoVs. Phylogeographic analyses of RdRp sequences show that several CoVs strains circulate in European bats: (i) old strains detected that have probably diverged a long time ago and are detected in different bat subspecies; (ii) strains detected in Myotis and Pipistrellus bat species that have more recently diverged. Our findings support previous observations describing the complexity of the detected CoVs in bats worldwide.
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Affiliation(s)
- Anne Goffard
- Molecular & Cellular Virology, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Bâtiment IBL. 1 rue du Pr. Calmette CS 50447, 59021 Lille Cedex, France.
| | - Christine Demanche
- Bacterial Respiratory Infections: Pertussis and Tuberculosis, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, F-59000 Lille, France.
| | - Laurent Arthur
- Museum d'Histoire Naturelle de Bourges, Les Rives d'Auron, allée René Ménard, 18000 Bourges, France.
| | - Claire Pinçon
- University Lille, CHU Lille, EA 2694-Santé publique: épidémiologie et qualité des soins, F-59000 Lille, France.
| | - Johan Michaux
- Conservation Genetics Unit, Institute of Botany (B. 22), University Liège, 4000 Liège, Belgium.
- CIRAD TA C-22/E-Campus international de Baillarguet, 34398 Montpellier Cedex 5, France.
| | - Jean Dubuisson
- Molecular & Cellular Virology, University Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille, Bâtiment IBL. 1 rue du Pr. Calmette CS 50447, 59021 Lille Cedex, France.
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Genetic drift of human coronavirus OC43 spike gene during adaptive evolution. Sci Rep 2015; 5:11451. [PMID: 26099036 PMCID: PMC4476415 DOI: 10.1038/srep11451] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 05/26/2015] [Indexed: 11/08/2022] Open
Abstract
Coronaviruses (CoVs) continuously threaten human health. However, to date, the evolutionary mechanisms that govern CoV strain persistence in human populations have not been fully understood. In this study, we characterized the evolution of the major antigen-spike (S) gene in the most prevalent human coronavirus (HCoV) OC43 using phylogenetic and phylodynamic analysis. Among the five known HCoV-OC43 genotypes (A to E), higher substitution rates and dN/dS values as well as more positive selection sites were detected in the S gene of genotype D, corresponding to the most dominant HCoV epidemic in recent years. Further analysis showed that the majority of substitutions were located in the S1 subunit. Among them, seven positive selection sites were chronologically traced in the temporal evolution routes of genotype D, and six were located around the critical sugar binding region in the N-terminal domain (NTD) of S protein, an important sugar binding domain of CoV. These findings suggest that the genetic drift of the S gene may play an important role in genotype persistence in human populations, providing insights into the mechanisms of HCoV-OC43 adaptive evolution.
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Kin N, Miszczak F, Lin W, Ar Gouilh M, Vabret A. Genomic Analysis of 15 Human Coronaviruses OC43 (HCoV-OC43s) Circulating in France from 2001 to 2013 Reveals a High Intra-Specific Diversity with New Recombinant Genotypes. Viruses 2015; 7:2358-77. [PMID: 26008694 PMCID: PMC4452910 DOI: 10.3390/v7052358] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Revised: 04/23/2015] [Accepted: 05/04/2015] [Indexed: 01/19/2023] Open
Abstract
Human coronavirus OC43 (HCoV-OC43) is one of five currently circulating human coronaviruses responsible for respiratory infections. Like all coronaviruses, it is characterized by its genome’s high plasticity. The objectives of the current study were to detect genetically distinct genotypes and eventually recombinant genotypes in samples collected in Lower Normandy between 2001 and 2013. To this end, we sequenced complete nsp12, S, and N genes of 15 molecular isolates of HCoV-OC43 from clinical samples and compared them to available data from the USA, Belgium, and Hong-Kong. A new cluster E was invariably detected from nsp12, S, and N data while the analysis of nsp12 and N genes revealed the existence of new F and G clusters respectively. The association of these different clusters of genes in our specimens led to the description of thirteen genetically distinct genotypes, among which eight recombinant viruses were discovered. Identification of these recombinant viruses, together with temporal analysis and tMRCA estimation, provides important information for understanding the dynamics of the evolution of these epidemic coronaviruses.
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Affiliation(s)
- Nathalie Kin
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-0-2-31-27-25-54
| | - Fabien Miszczak
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Wei Lin
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
| | - Meriadeg Ar Gouilh
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Institut Pasteur, Environment and Infectious Risks Research and Expertise Unit, F-75015 Paris, France
| | - Astrid Vabret
- Normandie Université, 14032 Caen, France; E-Mails: (F.M.); (M.A.G.); (A.V.)
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
- Department of Virology, University Hospital of Caen, F-14033 Caen, France
| | - Epicorem Consortium
- Université de Caen, Unité de Recherche Risques Microbiens (U2RM), F-14000 Caen, France; E-Mails: (W.L.); (E.C.)
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Fehr AR, Perlman S. Coronaviruses: an overview of their replication and pathogenesis. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2015. [PMID: 25720466 DOI: 10.1007/978‐1‐4939‐2438‐7_1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Anthony R Fehr
- Department of Microbiology, University of Iowa Carver College of Medicine, Iowa City, IA, 52242, USA
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Abstract
Coronaviruses (CoVs), enveloped positive-sense RNA viruses, are characterized by club-like spikes that project from their surface, an unusually large RNA genome, and a unique replication strategy. Coronaviruses cause a variety of diseases in mammals and birds ranging from enteritis in cows and pigs and upper respiratory disease in chickens to potentially lethal human respiratory infections. Here we provide a brief introduction to coronaviruses discussing their replication and pathogenicity, and current prevention and treatment strategies. We also discuss the outbreaks of the highly pathogenic Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and the recently identified Middle Eastern Respiratory Syndrome Coronavirus (MERS-CoV).
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Affiliation(s)
- Helena Jane Maier
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Erica Bickerton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
| | - Paul Britton
- grid.63622.330000000403887540The Pirbright Institute, Compton, United Kingdom
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Zhang Y, Li J, Xiao Y, Zhang J, Wang Y, Chen L, Paranhos-Baccalà G, Ren L, Wang J. Genotype shift in human coronavirus OC43 and emergence of a novel genotype by natural recombination. J Infect 2014; 70:641-50. [PMID: 25530469 PMCID: PMC7112537 DOI: 10.1016/j.jinf.2014.12.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 11/29/2014] [Accepted: 12/14/2014] [Indexed: 11/30/2022]
Abstract
Background Human coronavirus (HCoV) OC43 is the most prevalent HCoV in respiratory tract infections. Its molecular epidemiological characterization, particularly the genotyping, was poorly addressed. Methods The full-length spike (S), RNA-dependent RNA polymerase (RdRp), and nucleocapsid (N) genes were amplified from each respiratory sample collected from 65 HCoV-OC43-positive patients between 2005 and 2012. Genotypes were determined by phylogenetic analysis. Recombination was analyzed based on full-length viral genome sequences. Clinical manifestations of each HCoV genotype infection were compared by reviewing clinical records. Results Sixty of these 65 samples belong to genotypes B, C and D. The remaining five strains had incongruent positions in the phylogenetic trees of the S, RdRp and N genes, suggesting a novel genotype emerging, designated as genotype E. Whole genome sequencing and bootscan analysis indicated that genotype E is generated by recombination between genotypes B, C and D. Temporal analysis revealed a sequential genotype replacement of C, B, D and E over the study period with genotype D being the dominant genotype since 2007. The novel genotype E was only detected in children younger than three years suffering from lower respiratory tract infections. Conclusions Our results suggest that HCoV-OC43 genotypes are evolving. Such genotype shift may be an adapting mechanism for HCoV-OC43 maintaining its epidemic. Temporal shift of multiple human coronavirus OC43 genotypes. Emergence of a novel genotype E by natural recombination. Genotype D dominated HCoV-OC43 epidemic in China in recent years. Genotype evolving plays an important role in HCoV-OC43 epidemic.
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Affiliation(s)
- Yue Zhang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Jianguo Li
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Yan Xiao
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Jing Zhang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Ying Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | - Lan Chen
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China
| | | | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China.
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, PR China.
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Desforges M, Le Coupanec A, Stodola JK, Meessen-Pinard M, Talbot PJ. Human coronaviruses: viral and cellular factors involved in neuroinvasiveness and neuropathogenesis. Virus Res 2014; 194:145-58. [PMID: 25281913 PMCID: PMC7114389 DOI: 10.1016/j.virusres.2014.09.011] [Citation(s) in RCA: 236] [Impact Index Per Article: 23.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/22/2014] [Accepted: 09/24/2014] [Indexed: 12/15/2022]
Abstract
Human coronavirus (HCoV) are naturally neuroinvasive in both mice and humans. Both transneuronal and hematogenous route may allow virus invasion of the CNS. Infection of neurons leads to excitotoxicity, neurodegeneration and cell-death. HCoV are potentially associated with human neurological disorders.
Among the various respiratory viruses infecting human beings, coronaviruses are important pathogens, which usually infect the upper respiratory tract, where they are mainly associated with common colds. However, in more vulnerable populations, such as newborns, infants, the elderly and immune-compromised individuals, these opportunistic pathogens can also affect the lower respiratory tract, leading to pneumonia, exacerbations of asthma, and various types of respiratory distress syndrome. The respiratory involvement of human coronaviruses has been clearly established since the 1960s. Nevertheless, for almost three decades now, data reported in the scientific literature has also demonstrated that, like it was described for other human viruses, coronaviruses have neuroinvasive capacities since they can spread from the respiratory tract to the central nervous system (CNS). Once there, infection of CNS cells (neurotropism) could lead to human health problems, such as encephalitis and long-term neurological diseases. Neuroinvasive coronaviruses could damage the CNS as a result of misdirected host immune responses that could be associated with autoimmunity in susceptible individuals (virus-induced neuroimmunopathology) and/or viral replication, which directly induces damage to CNS cells (virus-induced neuropathology). Given all these properties, it has been suggested that these opportunistic human respiratory pathogens could be associated with the triggering or the exacerbation of neurologic diseases for which the etiology remains poorly understood. Herein, we present host and viral factors that participate in the regulation of the possible pathogenic processes associated with CNS infection by human coronaviruses and we try to decipher the intricate interplay between virus and host target cells in order to characterize their role in the virus life cycle as well as in the capacity of the cell to respond to viral invasion.
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Affiliation(s)
- Marc Desforges
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7.
| | - Alain Le Coupanec
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Jenny K Stodola
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Mathieu Meessen-Pinard
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7
| | - Pierre J Talbot
- Laboratory of Neuroimmunovirology, INRS-Institut Armand-Frappier, Institut national de la recherche scientifique, Université du Québec, 531 boulevard des Prairies, Laval, Québec, Canada H7V 1B7.
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Prevalence and genetic diversity analysis of human coronavirus OC43 among adult patients with acute respiratory infections in Beijing, 2012. PLoS One 2014; 9:e100781. [PMID: 24987849 PMCID: PMC4079595 DOI: 10.1371/journal.pone.0100781] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Accepted: 05/27/2014] [Indexed: 02/08/2023] Open
Abstract
To determine the prevalence, epidemiology and genetic diversity of human coronavirus OC43 (HCoV-OC43) among adult patients with acute respiratory infections (ARI) in Beijing,five hundred and fifty-nine nasopharyngeal swab samples were collected from adult patients with ARI in Beijing. The prevalence of HCoV-OC43 infection among these patients was assessed using two different OneStep reverse transcription polymerase chain reaction (RT-PCR) assays. The epidemiological profiles of the patients with HCoV-OC43 infection were described. Partial S and N genes of HCoV-OC43 circulating strains were sequenced followed by phylogenetic analysis and amino acid alignment. Our results showed that the prevalence of HCoV-OC43 infection was 12.52% (95% CI: 9.78–15.26%), and the epidemic peak occurred in autumn. Fifty partial S and 40 partial N fragments were obtained from these patients. Phylogenetic analysis based on neighbour-joining method showed that at least three distinct clusters (A, B, C/D) of HCoV-OC43 strains were circulating among adult patients with ARI in Beijing. In addition, some novel unique clusters (UNT) of HCoV-OC43 were found in the S- and N-based phylogenetic trees. Furthermore, consensus amino acids substitutes for each cluster were also found after alignment of partial S or N sequence coding region in this study. In conclusion, we herein describe the prevalence of HCoV-OC43 among adult patients and provide substantial evidence for the genetic diversity of HCoV-OC43 circulating in Beijing.
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Bidokhti MRM, Tråvén M, Krishna NK, Munir M, Belák S, Alenius S, Cortey M. Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains. J Gen Virol 2013; 94:2036-2049. [PMID: 23804565 DOI: 10.1099/vir.0.054940-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Coronaviruses demonstrate great potential for interspecies transmission, including zoonotic outbreaks. Although bovine coronavirus (BCoV) strains are frequently circulating in cattle farms worldwide, causing both enteric and respiratory disease, little is known about their genomic evolution. We sequenced and analysed the full-length spike (S) protein gene of 33 BCoV strains from dairy and feedlot farms collected during outbreaks that occurred from 2002 to 2010 in Sweden and Denmark. Amino acid identities were >97 % for the BCoV strains analysed in this work. These strains formed a clade together with Italian BCoV strains and were highly similar to human enteric coronavirus HECV-4408/US/94. A high similarity was observed between BCoV, canine respiratory coronavirus (CRCoV) and human coronavirus OC43 (HCoV-OC43). Molecular clock analysis of the S gene sequences estimated BCoV and CRCoV diverged from a common ancestor in 1951, while the time of divergence from a common ancestor of BCoV and HCoV-OC43 was estimated to be 1899. BCoV strains showed the lowest similarity to equine coronavirus, placing the date of divergence at the end of the eighteenth century. Two strongly positive selection sites were detected along the receptor-binding subunit of the S protein gene: spanning amino acid residues 109-131 and 495-527. By contrast, the fusion subunit was observed to be under negative selection. The selection pattern along the S glycoprotein implies adaptive evolution of BCoVs, suggesting a successful mechanism for BCoV to continuously circulate among cattle and other ruminants without disappearance.
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Affiliation(s)
- Mehdi R M Bidokhti
- Division of Ruminant Medicine and Veterinary Epidemiology, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07 Uppsala, Sweden
| | - Madeleine Tråvén
- Division of Ruminant Medicine and Veterinary Epidemiology, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07 Uppsala, Sweden
| | - Neel K Krishna
- Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, 700 West Olney Road, Norfolk, VA 23507-1696, USA
| | - Muhammad Munir
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.,Department of Virology, Immunobiology and Parasitology, National Veterinary Institute, Box 7028, SE-751 89 Uppsala, Sweden
| | - Sándor Belák
- Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden.,Department of Virology, Immunobiology and Parasitology, National Veterinary Institute, Box 7028, SE-751 89 Uppsala, Sweden
| | - Stefan Alenius
- Division of Ruminant Medicine and Veterinary Epidemiology, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07 Uppsala, Sweden
| | - Martí Cortey
- Department of Immunology, The Pirbright Institute, Ash Road, Pirbright GU24 0NF, UK
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Lei L, Ying S, Baojun L, Yi Y, Xiang H, Wenli S, Zounan S, Deyin G, Qingyu Z, Jingmei L, Guohui C. Attenuation of mouse hepatitis virus by deletion of the LLRKxGxKG region of Nsp1. PLoS One 2013; 8:e61166. [PMID: 23593419 PMCID: PMC3620170 DOI: 10.1371/journal.pone.0061166] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 03/08/2013] [Indexed: 11/19/2022] Open
Abstract
Coronaviruses are a family of large positive-sense RNA viruses that are responsible for a wide range of important veterinary and human diseases. Nsp1 has been shown to have an important role in the pathogenetic mechanisms of coronaviruses in vivo. To assess the function of a relatively conserved domain (LLRKxGxKG) of MHV nsp1, a mutant virus, MHV-nsp1-27D, with a 27 nts (LLRKxGxKG) deletion in nsp1, was constructed using a reverse genetic system with a vaccinia virus vector. The mutant virus had similar growth kinetics to MHV-A59 wild-type virus in 17CI-1 cells, but was highly attenuated in vivo. Moreover, the mutant virus completely protected C57BL/6 mice from a lethal MHV-A59 challenge. To further analyze the mechanism of the attenuation of the mutant virus, changes in reporter gene expression were measured in nsp1- or nsp1-27D-expressing cells; the results showed that nsp1 inhibited reporter gene expression controlled by different promoters, but that this inhibition was reduced for nsp1-27D. The research in vivo and in vitro suggests that the LLRKxGxKG region of nsp1 may play an important role in this process.
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Affiliation(s)
- Lin Lei
- State Key Laboratory of Pathogen and Biosecurity, Institute of Epidemiology and Microbiology, Academy of Millitary Medical Sciences, Beijing, China
| | - Sun Ying
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, China
| | - Luo Baojun
- State Key Laboratory of Pathogen and Biosecurity, Institute of Epidemiology and Microbiology, Academy of Millitary Medical Sciences, Beijing, China
| | - Yang Yi
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
| | - He Xiang
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
| | - Su Wenli
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
| | - Sun Zounan
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
| | - Guo Deyin
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan, China
| | - Zhu Qingyu
- State Key Laboratory of Pathogen and Biosecurity, Institute of Epidemiology and Microbiology, Academy of Millitary Medical Sciences, Beijing, China
| | - Liu Jingmei
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (LJ); (CG)
| | - Chang Guohui
- State Key Laboratory of Pathogen and Biosecurity, Institute of Epidemiology and Microbiology, Academy of Millitary Medical Sciences, Beijing, China
- Institute of Disease Prevention and Control, Academy of Military Medical Sciences, Beijing, China
- * E-mail: (LJ); (CG)
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Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. J Virol 2011; 85:11325-37. [PMID: 21849456 DOI: 10.1128/jvi.05512-11] [Citation(s) in RCA: 188] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Although human coronavirus OC43-OC43 (HCoV-OC43) is the coronavirus most commonly associated with human infections, little is known about its molecular epidemiology and evolution. We conducted a molecular epidemiology study to investigate different genotypes and potential recombination in HCoV-OC43. Twenty-nine HCoV-OC43 strains from nasopharyngeal aspirates, collected from 2004 to 2011, were subjected to RNA-dependent RNA polymerase (RdRp), spike, and nucleocapsid gene analysis. Phylogenetic analysis showed at least three distinct clusters of HCoV-OC43, although 10 unusual strains displayed incongruent phylogenetic positions between RdRp and spike genes. This suggested the presence of four HCoV-OC43 genotypes (A to D), with genotype D most likely arising from recombination. The complete genome sequencing of two genotype C and D strains and bootscan analysis showed recombination events between genotypes B and C in the generation of genotype D. Of the 29 strains, none belonged to the more ancient genotype A, 5 from 2004 belonged to genotype B, 15 from 2004 to 2006 belonged to genotype C, and 1 from 2004 and all 8 from 2008 to 2011 belonged to the recombinant genotype D. Molecular clock analysis using spike and nucleocapsid genes dated the most recent common ancestor of all genotypes to the 1950s, genotype B and C to the 1980s, genotype B to the 1990s, and genotype C to the late 1990s to early 2000s, while the recombinant genotype D strains were detected as early as 2004. This represents the first study to describe natural recombination in HCoV-OC43 and the evolution of different genotypes over time, leading to the emergence of novel genotype D, which is associated with pneumonia in our elderly population.
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Stanley M, Mayr J, Huber W, Vlasak R, Streicher H. Synthesis and inhibitory activity of sialic acid derivatives targeted at viral sialate-O-acetylesterases. Eur J Med Chem 2011; 46:2852-60. [PMID: 21524502 PMCID: PMC7111470 DOI: 10.1016/j.ejmech.2011.04.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 03/25/2011] [Accepted: 04/02/2011] [Indexed: 11/18/2022]
Abstract
A series of sialosides modified at the 4- and 9-hydroxy group were synthesised and tested for inhibition of the viral haemagglutinin-esterase activity from various Orthomyxoviruses and Coronaviruses. While no inhibition of the sialate-4-O-acetylesterases from mouse hepatitis virus strain S or sialodacryoadenitis virus was found, a 9-O-methyl derivative displayed inhibitory activity against recombinant sialate-9-O-acetylesterase from influenza C virus.
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Affiliation(s)
- Mathew Stanley
- Department of Chemistry and Biochemistry, University of Sussex, Brighton, BN1 9QG, UK
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