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Li KSM, Lau SKP, Woo PCY. Bats-The Magnificent Virus Player: SARS, MERS, COVID-19 and Beyond. Viruses 2023; 15:2342. [PMID: 38140583 PMCID: PMC10747191 DOI: 10.3390/v15122342] [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: 11/23/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Irrespective of whether COVID-19 originated from a natural or a genetically engineered virus, the ultimate source of Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is bats [...].
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Affiliation(s)
- Kenneth S. M. Li
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
| | - Susanna K. P. Lau
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
| | - Patrick C. Y. Woo
- Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (K.S.M.L.); (S.K.P.L.)
- Doctoral Program in Translational Medicine and Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan
- The iEGG and Animal Biotechnology Research Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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Zhu DX, Stallings CL. Transcription regulation by CarD in mycobacteria is guided by basal promoter kinetics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.16.533025. [PMID: 36993566 PMCID: PMC10055060 DOI: 10.1101/2023.03.16.533025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2023]
Abstract
Bacterial pathogens like Mycobacterium tuberculosis ( Mtb ) employ transcription factors to adapt their physiology to the diverse environments within their host. CarD is a conserved bacterial transcription factor that is essential for viability in Mtb . Unlike classical transcription factors that recognize promoters by binding to specific DNA sequence motifs, CarD binds directly to the RNA polymerase (RNAP) to stabilize the open complex intermediate (RP o ) during transcription initiation. We previously showed using RNA-sequencing that CarD is capable of both activating and repressing transcription in vivo . However, it is unknown how CarD achieves promoter specific regulatory outcomes in Mtb despite binding indiscriminate of DNA sequence. We propose a model where CarD's regulatory outcome depends on the promoter's basal RP o stability and test this model using in vitro transcription from a panel of promoters with varying levels of RP o stability. We show that CarD directly activates full-length transcript production from the Mtb ribosomal RNA promoter rrnA P3 (AP3) and that the degree of transcription activation by CarD is negatively correlated with RP o stability. Using targeted mutations in the extended -10 and discriminator region of AP3, we show that CarD directly represses transcription from promoters that form relatively stable RP o . DNA supercoiling also influenced RP o stability and affected the direction of CarD regulation, indicating that the outcome of CarD activity can be regulated by factors beyond promoter sequence. Our results provide experimental evidence for how RNAP-binding transcription factors like CarD can exert specific regulatory outcomes based on the kinetic properties of a promoter.
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Zapatero Gaviria A, Barba Martin R. What do we know about the origin of COVID-19 three years later? Rev Clin Esp 2023; 223:240-243. [PMID: 36933695 PMCID: PMC10019034 DOI: 10.1016/j.rceng.2023.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 02/17/2023] [Indexed: 03/18/2023]
Abstract
More than three years have passed since the first case of a new coronavirus infection (SARS-CoV-2) in the city of Wuhan (Hubei, China). The Wuhan Institute of Virology was founded in that city in 1956 and the country's first biosafety level 4 laboratory opened within that center in 2015. The coincidence that the first cases of infection emerged in the city where the virology institute's headquarters is located, the failure to 100% identify the virus' RNA in any of the coronaviruses isolated in bats, and the lack of evidence on a possible intermediate animal host in the contagion's transmission make it so that at present, there are doubts about the real origin of SARS-CoV-2. This article will review two theories: SARS-CoV-2 as a virus of zoonotic origin or as a leak from the high-level biosafety laboratory in Wuhan.
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Affiliation(s)
- A Zapatero Gaviria
- Servicio Medicina Interna, Hospital Universitario Fuenlabrada, Universidad Rey Juan Carlos.
| | - R Barba Martin
- Servicio Medicina Interna, Hospital Universitario Rey Juan Carlos, Universidad Rey Juan Carlos
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Rahman S, Ullah S, Shinwari ZK, Ali M. Bats-associated beta-coronavirus detection and characterization: First report from Pakistan. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 108:105399. [PMID: 36584905 PMCID: PMC9793958 DOI: 10.1016/j.meegid.2022.105399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/22/2022] [Accepted: 12/26/2022] [Indexed: 12/28/2022]
Abstract
Bats remains as reservoirs for highly contagious and pathogenic viral families including the Coronaviridae, Filoviridae, Paramyxoviruses, and Rhabdoviridae. Spill over of viral species (SARS-CoV, MERS-CoV & SARS-CoV2) from bats (as a possible potential reservoirs) have recently caused worst outbreaks. Early detection of viral species of pandemic potential in bats is of great importance. We detected beta coronaviruses in the studied bats population (positive samples from Rousettus leschenaultia) and performed the evolutionary analysis, amino acid sequence alignment, and analysed the 3-Dimentional protein structure. We detected the coronaviruses for the first time in bats from Pakistan. Our analysis based on RdRp partial gene sequencing suggest that the studied viral strains are closely related to MERS-CoV-like viruses as they exhibit close structure similarities (with few substitutions) and also observed a substitution in highly conserved SDD in the palm subdomain of motif C to ADD, when compared with earlier reported viral strains. It could be concluded from our study that coronaviruses are circulating among the bat's population in Pakistan. Based on the current findings, we suggest large scale screening procedures of bat virome across the country to detect potential pathogenic viral species.
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Affiliation(s)
- Sidra Rahman
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan.
| | - Sana Ullah
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan; Natural and Medical Sciences Research Center, University of Nizwa, Oman.
| | | | - Muhammad Ali
- Department of Biotechnology, Quaid-i-Azam University, Islamabad, Pakistan.
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Jones A, Zhang D, Massey SE, Deigin Y, Nemzer LR, Quay SC. Discovery of a novel merbecovirus DNA clone contaminating agricultural rice sequencing datasets from Wuhan, China. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.12.528210. [PMID: 36865340 PMCID: PMC9979991 DOI: 10.1101/2023.02.12.528210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.
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Wang X, Bao M, Xu N, Sun R, Dai W, Sun K, Wang H, Feng J. Full-Length Transcriptome of Myotis pilosus as a Reference Resource and Mining of Auditory and Immune Related Genes. Int J Mol Sci 2022; 24:ijms24010062. [PMID: 36613506 PMCID: PMC9820712 DOI: 10.3390/ijms24010062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 12/11/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Rickett's big-footed bat, Myotis pilosus, which belongs to the family Vespertilionida, is the only known piscivorous bat in East Asia. Accurate whole genome and transcriptome annotations are essential for the study of bat biological evolution. The lack of a whole genome for M. pilosus has limited our understanding of the molecular mechanisms underlying the species' evolution, echolocation, and immune response. In the present work, we sequenced the entire transcriptome using error-corrected PacBio single-molecule real-time (SMRT) data. Then, a total of 40 GB of subreads were generated, including 29,991 full-length non-chimeric (FLNC) sequences. After correction by Illumina short reads and de-redundancy, we obtained 26,717 error-corrected isoforms with an average length of 3018.91 bp and an N50 length of 3447 bp. A total of 1528 alternative splicing (AS) events were detected by transcriptome structural analysis. Furthermore, 1032 putative transcription factors (TFs) were identified, with additional identification of several long non-coding RNAs (lncRNAs) with high confidence. Moreover, several key genes, including PRL-2, DPP4, Glul, and ND1 were also identified as being associated with metabolism, immunity, nervous system processes, and auditory perception. A multitude of pattern recognition receptors was identified, including NLR, RLR, SRCR, the antiviral molecule IRF3, and the IFN receptor subunit IFNAR1. High-quality reference genomes at the transcriptome level may be used to quantify gene or transcript expression, evaluate alternative splicing levels, identify novel transcripts, and enhance genome annotation in bats.
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Affiliation(s)
- Xue Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Mingyue Bao
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Ningning Xu
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Ruyi Sun
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
| | - Hui Wang
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (H.W.); (J.F.)
| | - Jiang Feng
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Correspondence: (H.W.); (J.F.)
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Zhu Y, Binder J, Yurgelonis I, Rai DK, Lazarro S, Costales C, Kobylarz K, McMonagle P, Steppan CM, Aschenbrenner L, Anderson AS, Cardin RD. Generation of a VeroE6 Pgp gene knock out cell line and its use in SARS-CoV-2 antiviral study. Antiviral Res 2022; 208:105429. [PMID: 36208677 PMCID: PMC9533647 DOI: 10.1016/j.antiviral.2022.105429] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/28/2022] [Accepted: 10/02/2022] [Indexed: 11/25/2022]
Abstract
Vero cells are widely used for antiviral tests and virology research for SARS-CoV-2 as well as viruses from various other families. However, Vero cells generally express high levels of multi-drug resistance 1 (MDR1) or Pgp protein, the efflux transporter of foreign substances including many antiviral compounds, affecting the antiviral activity as well as interpretation of data. To address this, a Pgp gene knockout VeroE6 cell line (VeroE6-Pgp-KO) was generated using CRISPR-CAS9 technology. These cells no longer expressed the Pgp protein as indicated by flow cytometry analysis following staining with a Pgp-specific monoclonal antibody. They also showed significantly reduced efflux transporter activity in the calcein acetoxymethyl ester (calcein AM) assay. The VeroE6-Pgp-KO cells and the parental VeroE6 cells were each infected with SARS-CoV-2 to test antiviral activities of remdesivir and nirmatrelvir, two known Pgp substrates, in the presence or absence of a Pgp inhibitor. The compounds showed antiviral activities in VeroE6-Pgp-KO cells similar to that observed in the presence of the Pgp inhibitor. Thus, the newly established VeroE6-Pgp-KO cell line adds a new in vitro virus infection system for SARS-CoV-2 and possibly other viruses to test antiviral therapies without a need to control the Pgp activity. Removal of the Pgp inhibitor for antiviral assays will lead to less data variation and prevent failed assays.
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Affiliation(s)
- Yuao Zhu
- Pfizer Inc, 401 N Middletown Rd, Pearl River, NY, 10965, USA,Corresponding author
| | - Joe Binder
- Pfizer Inc, 401 N Middletown Rd, Pearl River, NY, 10965, USA
| | | | - Devendra K. Rai
- Pfizer Inc, 401 N Middletown Rd, Pearl River, NY, 10965, USA
| | - Sarah Lazarro
- Pfizer Inc, 445 Eastern Point Rd, Groton, CT, 06333, USA
| | | | - Keith Kobylarz
- Pfizer Inc, 401 N Middletown Rd, Pearl River, NY, 10965, USA
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Ramanantsalama RV, Goodman SM, Dietrich M, Lebarbenchon C. Interaction between Old World fruit bats and humans: From large scale ecosystem services to zoonotic diseases. Acta Trop 2022; 231:106462. [PMID: 35421381 DOI: 10.1016/j.actatropica.2022.106462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 04/07/2022] [Accepted: 04/09/2022] [Indexed: 11/01/2022]
Abstract
The Old World tropical and subtropical frugivorous bat genus Rousettus (Pteropodidae) contains species with broad distributions, as well as those occurring in restricted geographical areas, particularly islands. Herein we review the role of Rousettus as a keystone species from a global "One Health" approach and related to ecosystem functioning, zoonotic disease and public health. Rousettus are efficient at dispersing seeds and pollinating flowers; their role in forest regeneration is related to their ability to fly considerable distances during nightly foraging bouts and their relatively small body size, which allows them to access fruits in forested areas with closed vegetation. Rousettus are also reservoirs for various groups of pathogens (viruses, bacteria, fungi, protozoa), which, by definition, are infectious agents causing disease. The study of day roosts of different species of Rousettus and the successful establishment of captive breeding colonies have provided important details related to the infection dynamics of their associated pathogens. Large-scale conversion of forested areas into agricultural landscapes has increased contact between humans and Rousettus, therefore augmenting the chances of infectious agent spillover. Many crucial scientific details are still lacking related to members of this genus, which have direct bearing on the prevention of emerging disease outbreaks, as well as the conservation of these bats. The public should be better informed on the capacity of fruit bats as keystone species for large scale forest regeneration and in spreading pathogens. Precise details on the transmission of zoonotic diseases of public health importance associated with Rousettus should be given high priority.
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Auerswald H, Low DHW, Siegers JY, Ou T, Kol S, In S, Linster M, Su YCF, Mendenhall IH, Duong V, Smith GJD, Karlsson EA. A Look inside the Replication Dynamics of SARS-CoV-2 in Blyth's Horseshoe Bat ( Rhinolophus lepidus) Kidney Cells. Microbiol Spectr 2022; 10:e0044922. [PMID: 35638834 PMCID: PMC9241725 DOI: 10.1128/spectrum.00449-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 05/11/2022] [Indexed: 01/09/2023] Open
Abstract
Bats are considered the natural reservoir of numerous emerging viruses such as severe acute respiratory syndrome coronaviruses (SARS-CoVs). There is a need for immortalized bat cell lines to culture and investigate the pathogenicity, replication kinetics, and evolution of emerging coronaviruses. We illustrate the susceptibility and permissiveness of a spontaneously immortalized kidney cell line (Rhileki) from Blyth's horseshoe bat (R. lepidus) to SARS-CoV-2 virus, including clinical isolates, suggesting a possible virus-host relationship. We were able to observe limited SARS-CoV-2 replication in Rhileki cells compared with simian VeroE6 cells. Slower viral replication in Rhileki cells was indicated by higher ct values (RT-PCR) at later time points of the viral culture and smaller foci (foci forming assay) compared with those of VeroE6 cells. With this study we demonstrate that SARS-CoV-2 replication is not restricted to R. sinicus and could include more Rhinolophus species. The establishment of a continuous Rhinolophus lepidus kidney cell line allows further characterization of SARS-CoV-2 replication in Rhinolophus bat cells, as well as isolation attempts of other bat-borne viruses. IMPORTANCE The current COVID-19 pandemic demonstrates the significance of bats as reservoirs for severe viral diseases. However, as bats are difficult to establish as animal models, bat cell lines can be an important proxy for the investigation of bat-virus interactions and the isolation of bat-borne viruses. This study demonstrates the susceptibility and permissiveness of a continuous kidney bat cell line to SARS-CoV-2. This does not implicate the bat species Rhinolophus lepidus, where these cells originate from, as a potential reservoir, but emphasizes the usefulness of this cell line for further characterization of SARS-CoV-2. This can lead to a better understanding of emerging viruses that could cause significant disease in humans and domestic animals.
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Affiliation(s)
- Heidi Auerswald
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Dolyce H. W. Low
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Jurre Y. Siegers
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Teyputita Ou
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Sonita Kol
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Saraden In
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Martin Linster
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Yvonne C. F. Su
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
| | - Ian H. Mendenhall
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
| | - Veasna Duong
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
| | - Gavin J. D. Smith
- Programme in Emerging Infectious Diseases, Duke-NUS Medical School, Singapore
- SingHealth Duke-NUS Global Health Institute, SingHealth Duke-NUS Academic Medical Centre, Singapore
- Duke Global Health Institute, Duke University, Durham, North Carolina, USA
| | - Erik A. Karlsson
- Virology Unit, Institut Pasteur du Cambodge, Institut Pasteur International Network, Phnom Penh, Cambodia
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K A, Sharma A, Kumar D, Singh SK, Gupta G, Chellappan DK, Dua K, Nagraik R. Molecular aspects of Omicron, vaccine development, and recombinant strain XE: A review. J Med Virol 2022; 94:4628-4643. [PMID: 35705439 PMCID: PMC9349635 DOI: 10.1002/jmv.27936] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 12/19/2022]
Abstract
The global pandemic of COVID‐19 began in December 2019 and is still continuing. The past 2 years have seen the emergence of several variants that were more vicious than each other. The emergence of Omicron (B.1.1.529) proved to be a huge epidemiological concern as the rate of infection of this particular strain was enormous. The strain was identified in South Africa on November 24, 2021 and was classified as a “Variant of Concern” on November 26, 2021. The Omicron variant possessed mutations in the key RBD region, the S region, thereby increasing the affinity of ACE2 for better transmission of the virus. Antibody resistance was found in this variant and it was able to reduce vaccine efficiency of vaccines. The need for a booster vaccine was brought forth due to the prevalence of the Omicron variant and, subsequently, this led to targeted research and development of variant‐specific vaccines and booster dosage. This review discusses broadly the genomic characters and features of Omicron along with its specific mutations, evolution, antibody resistance, and evasion, utilization of CRISPR‐Cas12a assay for Omicron detection, T‐cell immunity elicited by vaccines against Omicron, and strategies to decrease Omicron infection along with COVID‐19 and it also discusses on XE recombinant variant and on infectivity of BA.2 subvariant of Omicron.
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Affiliation(s)
- Akash K
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Avinash Sharma
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
| | - Deepak Kumar
- Department of Pharmaceutical Chemistry, School of Pharmaceutical SciencesShoolini UniversitySolanHimachal PradeshIndia
| | - Sachin K. Singh
- School of Pharmaceutical SciencesLovely Professional UniversityPhagwara, PunjabIndia
| | - Gaurav Gupta
- School of PharmacySuresh Gyan Vihar UniversityJagatpura, JaipurIndia
- Uttaranchal Institute of Pharmaceutical SciencesUttaranchal UniversityDehradunIndia
- Department of Pharmacology, Saveetha Dental College, Saveetha Institute of Medical and Technical SciencesSaveetha UniversityChennaiIndia
| | | | - Kamal Dua
- Faculty of Health, Australian Research Centre in Complementary and Integrative MedicineUniversity of Technology SydneyUltimoNSWAustralia
- Discipline of Pharmacy Graduate School of HealthUniversity of Technology SydneyUltimoNSWAustralia
| | - Rupak Nagraik
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and BiotechnologyShoolini UniversitySolanHimachal PradeshIndia
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Interspecies Jumping of Bat Coronaviruses. Viruses 2021; 13:v13112188. [PMID: 34834994 PMCID: PMC8620431 DOI: 10.3390/v13112188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
In the last two decades, several coronavirus (CoV) interspecies jumping events have occurred between bats and other animals/humans, leading to major epidemics/pandemics and high fatalities. The SARS epidemic in 2002/2003 had a ~10% fatality. The discovery of SARS-related CoVs in horseshoe bats and civets and genomic studies have confirmed bat-to-civet-to-human transmission. The MERS epidemic that emerged in 2012 had a ~35% mortality, with dromedaries as the reservoir. Although CoVs with the same genome organization (e.g., Tylonycteris BatCoV HKU4 and Pipistrellus BatCoV HKU5) were also detected in bats, there is still a phylogenetic gap between these bat CoVs and MERS-CoV. In 2016, 10 years after the discovery of Rhinolophus BatCoV HKU2 in Chinese horseshoe bats, fatal swine disease outbreaks caused by this virus were reported in southern China. In late 2019, an outbreak of pneumonia emerged in Wuhan, China, and rapidly spread globally, leading to >4,000,000 fatalities so far. Although the genome of SARS-CoV-2 is highly similar to that of SARS-CoV, patient zero and the original source of the pandemic are still unknown. To protect humans from future public health threats, measures should be taken to monitor and reduce the chance of interspecies jumping events, either occurring naturally or through recombineering experiments.
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12
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Farrag MA, Amer HM, Bhat R, Almajhdi FN. Sequence and phylogentic analysis of MERS-CoV in Saudi Arabia, 2012-2019. Virol J 2021; 18:90. [PMID: 33931099 PMCID: PMC8085657 DOI: 10.1186/s12985-021-01563-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/22/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The Middle East Respiratory Syndrome-related Coronavirus (MERS-CoV) continues to exist in the Middle East sporadically. Thorough investigations of the evolution of human coronaviruses (HCoVs) are urgently required. In the current study, we studied amplified fragments of ORF1a/b, Spike (S) gene, ORF3/4a, and ORF4b of four human MERS-CoV strains for tracking the evolution of MERS-CoV over time. METHODS RNA isolated from nasopharyngeal aspirate, sputum, and tracheal swabs/aspirates from hospitalized patients with suspected MERS-CoV infection were analyzed for amplification of nine variable genomic fragments. Sequence comparisons were done using different bioinformatics tools available. RESULTS Several mutations were identified in ORF1a/b, ORF3/4a and ORF4b, with the highest mutation rates in the S gene. Five codons; 4 in ORF1a and 1 in the S gene, were found to be under selective pressure. Characteristic amino acid changes, potentially hosted and year specific were defined across the S protein and in the receptor-binding domain Phylogenetic analysis using S gene sequence revealed clustering of MERS-CoV strains into three main clades, A, B and C with subdivision of with clade B into B1 to B4. CONCLUSIONS In conclusion, MERS-CoV appears to continuously evolve. It is recommended that the molecular and pathobiological characteristics of future MERS-CoV strains should be analyzed on regular basis to prevent potential future outbreaks at early phases.
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Affiliation(s)
- Mohamed A Farrag
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Haitham M Amer
- Department of Virology, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Rauf Bhat
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Fahad N Almajhdi
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia.
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Zhang HL, Li YM, Sun J, Zhang YY, Wang TY, Sun MX, Wang MH, Yang YL, Hu XL, Tang YD, Zhao J, Cai X. Evaluating angiotensin-converting enzyme 2-mediated SARS-CoV-2 entry across species. J Biol Chem 2021; 296:100435. [PMID: 33610551 PMCID: PMC7892319 DOI: 10.1016/j.jbc.2021.100435] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 02/10/2021] [Accepted: 02/16/2021] [Indexed: 01/01/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents a global threat, and the interaction between the virus and angiotensin-converting enzyme 2 (ACE2), the primary entry receptor for SARS-CoV-2, is a key determinant of the range of hosts that can be infected by the virus. However, the mechanisms underpinning ACE2-mediated viral entry across species remains unclear. Using infection assay, we evaluated SARS-CoV-2 entry mediated by ACE2 of 11 different animal species. We discovered that ACE2 of Rhinolophus sinicus (Chinese rufous horseshoe bat), Felis catus (domestic cat), Canis lupus familiaris (dog), Sus scrofa (wild pig), Capra hircus (goat), and Manis javanica (Malayan pangolin) facilitated SARS-CoV-2 entry into nonsusceptible cells. Moreover, ACE2 of the pangolin also mediated SARS-CoV-2 entry, adding credence to the hypothesis that SARS-CoV-2 may have originated from pangolins. However, the ACE2 proteins of Rhinolophus ferrumequinum (greater horseshoe bat), Gallus gallus (red junglefowl), Notechis scutatus (mainland tiger snake), or Mus musculus (house mouse) did not facilitate SARS-CoV-2 entry. In addition, a natural isoform of the ACE2 protein of Macaca mulatta (rhesus monkey) with the Y217N mutation was resistant to SARS-CoV-2 infection, highlighting the possible impact of this ACE2 mutation on SARS-CoV-2 studies in rhesus monkeys. We further demonstrated that the Y217 residue of ACE2 is a critical determinant for the ability of ACE2 to mediate SARS-CoV-2 entry. Overall, these results clarify that SARS-CoV-2 can use the ACE2 receptors of multiple animal species and show that tracking the natural reservoirs and intermediate hosts of SARS-CoV-2 is complex.
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Affiliation(s)
- Hong-Liang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yu-Ming Li
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Yu-Yuan Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Tong-Yun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Ming-Xia Sun
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Meng-Hang Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yue-Lin Yang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xiao-Liang Hu
- School of Life Sciences and Food Engineering, Yibin University, Yibin Key Laboratory of Zoological Diversity and Ecological Conservation, Yibin, China
| | - Yan-Dong Tang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Disease, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China.
| | - Xuehui Cai
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute of Chinese Academy of Agricultural Sciences, Harbin, China.
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Isolation of MERS-related coronavirus from lesser bamboo bats that uses DPP4 and infects human-DPP4-transgenic mice. Nat Commun 2021; 12:216. [PMID: 33431849 PMCID: PMC7801609 DOI: 10.1038/s41467-020-20458-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/27/2020] [Indexed: 12/26/2022] Open
Abstract
While a number of human coronaviruses are believed to be originated from ancestral viruses in bats, it remains unclear if bat coronaviruses are ready to cause direct bat-to-human transmission. Here, we report the isolation of a MERS-related coronavirus, Tylonycteris-bat-CoV-HKU4, from lesser bamboo bats. Tylonycteris-bat-CoV-HKU4 replicates efficiently in human colorectal adenocarcinoma and hepatocarcinoma cells with cytopathic effects, and can utilize human-dipeptidyl-peptidase-4 and dromedary camel-dipeptidyl-peptidase-4 as the receptors for cell entry. Flow cytometry, co-immunoprecipitation and surface plasmon resonance assays show that Tylonycteris-bat-CoV-HKU4-receptor-binding-domain can bind human-dipeptidyl-peptidase-4, dromedary camel-dipeptidyl-peptidase-4, and Tylonycteris pachypus-dipeptidyl-peptidase-4. Tylonycteris-bat-CoV-HKU4 can infect human-dipeptidyl-peptidase-4-transgenic mice by intranasal inoculation with self-limiting disease. Positive virus and inflammatory changes were detected in lungs and brains of infected mice, associated with suppression of antiviral cytokines and activation of proinflammatory cytokines and chemokines. The results suggest that MERS-related bat coronaviruses may overcome species barrier by utilizing dipeptidyl-peptidase-4 and potentially emerge in humans by direct bat-to-human transmission. Several human coronaviruses (CoV) have been proposed to emerge from bats but evidence of direct bat-to-human transmission is slim. In this work, the authors isolate a MERS-related CoV strain directly from bats and show that it infects target cells in vitro and engineered mice through the human DDP4 receptor.
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15
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Meng X, Lou QY, Yang WY, Chen R, Xu WH, Yang Y, Zhang L, Xu T, Xiang HF. Gordian Knot: Gastrointestinal lesions caused by three highly pathogenic coronaviruses from SARS-CoV and MERS-CoV to SARS-CoV-2. Eur J Pharmacol 2021; 890:173659. [PMID: 33131637 PMCID: PMC7581377 DOI: 10.1016/j.ejphar.2020.173659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/25/2020] [Accepted: 10/20/2020] [Indexed: 12/23/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen of 2019 novel coronavirus disease (COVID-19), is currently spreading around the world. The WHO declared on January 31 that the outbreak of SARS-CoV-2 was a public health emergency. SARS-Cov-2 is a member of highly pathogenic coronavirus group that also consists of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Although respiratory tract lesions were regarded as main manifestation of SARS-Cov-2 infection, gastrointestinal lesions were also reported. Similarly, patients with SARS-CoV and MERS-CoV were also observed. Common gastrointestinal symptoms of patients mainly included diarrhea, vomiting and abdominal pain. Gastrointestinal lesions could be used as basis for early diagnosis of patients, and at the same time, controlling gastrointestinal lesions better facilitated to cut off the route of fecal-oral transmission. Hence, this review summarizes the characteristics and mechanism of gastrointestinal lesions caused by three highly pathogenic human coronavirus infections including SARS-CoV, MERS-CoV, as well as SARS-CoV-2. Furthermore, it is expected to gain experience from gastrointestinal lesions caused by SARS-CoV and MERS-CoV infections in order to be able to better relieve SARS-CoV-2 epidemic. Targetin gut microbiota to regulate the process of SARS-CoV-2 infection should be a concern. Especially, the application of nanotechnology may provide help for further controlling COVID-19.
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Affiliation(s)
- Xiang Meng
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Qiu-Yue Lou
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, 230032, China.
| | - Wen-Ying Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Ran Chen
- School of Stomatology, Anhui Medical University, Hefei, 230032, China.
| | - Wen-Hua Xu
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China.
| | - Yang Yang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China; Periodontal Department, Anhui Stomatology Hospital Affiliated to Anhui Medical University, Hefei, 230032, China.
| | - Lei Zhang
- College & Hospital of Stomatology, Anhui Medical University, Key Lab. of Oral Diseases Research of Anhui Province, Hefei, 230032, China; Periodontal Department, Anhui Stomatology Hospital Affiliated to Anhui Medical University, Hefei, 230032, China.
| | - Tao Xu
- School of Pharmacy, Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei, 230032, China; Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Hefei, P.R. China.
| | - Hui-Fen Xiang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China.
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16
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Din A, Li Y, Khan T, Zaman G. Mathematical analysis of spread and control of the novel corona virus (COVID-19) in China. CHAOS, SOLITONS, AND FRACTALS 2020; 141:110286. [PMID: 32989346 PMCID: PMC7510499 DOI: 10.1016/j.chaos.2020.110286] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/26/2020] [Accepted: 09/08/2020] [Indexed: 05/05/2023]
Abstract
Number of well-known contagious diseases exist around the world that mainly include HIV, Hepatitis B, influenzas etc., among these, a recently contested coronavirus (COVID-19) is a serious class of such transmissible syndromes. Abundant scientific evidence the wild animals are believed to be the primary hosts of the virus. Majority of such cases are considered to be human-to-human transmission, while a few are due to wild animals-to-human transmission and substantial burdens on healthcare system following this spread. To understand the dynamical behavior such diseases, we fitted a susceptible-infectious-quarantined model for human cases with constant proportions. We proposed a model that provide better constraints on understanding the climaxes of such unseen disastrous spread, relevant consequences, and suggesting future imperative strategies need to be adopted. The main features of the work include the positivity, boundedness, existence and uniqueness of solution of the model. The conditions were derived under which the COVID-19 may extinct or persist in the population. Sensitivity and estimation of those important parameters have been carried out that plays key role in the transmission mechanism. To optimize the spread of such disease, we present a control problem for further analysis using two control measures. The necessary conditions have been derived using the Pontryagin's maximum principle. Parameter values have been estimated from the real data and experimental numerical simulations are presented for comparison as well as verification of theoretical results. The obtained numerical results also present the verification, accuracy, validation, and robustness of the proposed scheme.
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Affiliation(s)
- Anwarud Din
- Department of Mathematics Sun Yat-sen University Guangzhou, 510275 P. R. China
| | - Yongjin Li
- Department of Mathematics Sun Yat-sen University Guangzhou, 510275 P. R. China
| | - Tahir Khan
- Department of Mathematics, University of Malakand, Chakdara, Pakistan
| | - Gul Zaman
- Department of Mathematics, University of Malakand, Chakdara, Pakistan
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17
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Masood N, Malik SS, Raja MN, Mubarik S, Yu C. Unraveling the Epidemiology, Geographical Distribution, and Genomic Evolution of Potentially Lethal Coronaviruses (SARS, MERS, and SARS CoV-2). Front Cell Infect Microbiol 2020; 10:499. [PMID: 32974224 PMCID: PMC7481402 DOI: 10.3389/fcimb.2020.00499] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 08/11/2020] [Indexed: 12/11/2022] Open
Abstract
SARS CoV appeared in 2003 in China, transmitted from bats to humans via eating infected animals. It affected 8,096 humans with a death rate of 11% affecting 21 countries. The receptor binding domain (RBD) in S protein of this virus gets attached with the ACE2 receptors present on human cells. MERS CoV was first reported in 2012 in Middle East, originated from bat and transmitted to humans through camels. MERS CoV has a fatality rate of 35% and last case reported was in 2017 making a total of 1,879 cases worldwide. DPP4 expressed on human cells is the main attaching site for RBD in S protein of MERS CoV. Folding of RBD plays a crucial role in its pathogenesis. Virus causing COVID-19 was named as SARS CoV-2 due its homology with SARS CoV that emerged in 2003. It has become a pandemic affecting nearly 200 countries in just 3 months' time with a death rate of 2-3% currently. The new virus is fast spreading, but it utilizes the same RBD and ACE2 receptors along with furin present in human cells. The lessons learned from the SARS and MERS epidemics are the best social weapons to face and fight against this novel global threat.
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Affiliation(s)
- Nosheen Masood
- Department of Biotechnology, Fatima Jinnah Women University, Rawalpindi, Pakistan
| | | | | | - Sumaira Mubarik
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, China
| | - Chuanhua Yu
- Department of Epidemiology and Biostatistics, School of Health Sciences, Wuhan University, Wuhan, China
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18
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Management of epigenomic networks entailed in coronavirus infections and COVID-19. Clin Epigenetics 2020; 12:118. [PMID: 32758273 PMCID: PMC7404079 DOI: 10.1186/s13148-020-00912-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
Coronaviruses (CoVs) are highly diverse single-stranded RNA viruses owing to their susceptibility to numerous genomic mutations and recombination. Such viruses involve human and animal pathogens including the etiologic agents of acute respiratory tract illnesses: severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and the highly morbific SARS-CoV-2. Coronavirus disease 2019 (COVID-19), an emerging disease with a quick rise in infected cases and deaths, was recently identified causing a worldwide pandemic. COVID-19 disease outcomes were found to increase in elderly and patients with a compromised immune system. Evidences indicated that the main culprit behind COVID-19 deaths is the cytokine storm, which is illustrated by an uncontrolled over-production of soluble markers of inflammation. The regulation process of coronavirus pathogenesis through molecular mechanism comprise virus-host interactions linked to viral entry, replication and transcription, escape, and immune system control. Recognizing coronavirus infections and COVID-19 through epigenetics lens will lead to potential alteration in gene expression thus limiting coronavirus infections. Focusing on epigenetic therapies reaching clinical trials, clinically approved epigenetic-targeted agents, and combination therapy of antivirals and epigenetic drugs is currently considered an effective and valuable approach for viral replication and inflammatory overdrive control.
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19
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Lau SK, Wong AC, Luk HK, Li KS, Fung J, He Z, Cheng FK, Chan TT, Chu S, Aw-Yong KL, Lau TC, Fung KS, Woo PC. Differential Tropism of SARS-CoV and SARS-CoV-2 in Bat Cells. Emerg Infect Dis 2020; 26:2961-2965. [PMID: 32730733 PMCID: PMC7706959 DOI: 10.3201/eid2612.202308] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 did not replicate efficiently in 13 bat cell lines, whereas severe acute respiratory syndrome coronavirus replicated efficiently in kidney cells of its ancestral host, the Rhinolophus sinicus bat, suggesting different evolutionary origins. Structural modeling showed that RBD/RsACE2 binding may contribute to the differential cellular tropism.
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20
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Mou H, Quinlan BD, Peng H, Guo Y, Peng S, Zhang L, Davis-Gardner ME, Gardner MR, Crynen G, Voo ZX, Bailey CC, Alpert MD, Rader C, Choe H, Farzan M. Mutations from bat ACE2 orthologs markedly enhance ACE2-Fc neutralization of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.29.178459. [PMID: 32637954 PMCID: PMC7337384 DOI: 10.1101/2020.06.29.178459] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike (S) protein mediates infection of cells expressing angiotensin-converting enzyme 2 (ACE2). ACE2 is also the viral receptor of SARS-CoV (SARS-CoV-1), a related coronavirus that emerged in 2002-2003. Horseshoe bats (genus Rhinolophus ) are presumed to be the original reservoir of both viruses, and a SARS-like coronavirus, RaTG13, closely related SARS-CoV-2, has been isolated from one horseshoe-bat species. Here we characterize the ability of S-protein receptor-binding domains (RBDs) of SARS-CoV-1, SARS-CoV-2, and RaTG13 to bind a range of ACE2 orthologs. We observed that the SARS-CoV-2 RBD bound human, pangolin, and horseshoe bat ( R. macrotis) ACE2 more efficiently than the SARS-CoV-1 or RaTG13 RBD. Only the RaTG13 RBD bound rodent ACE2 orthologs efficiently. Five mutations drawn from ACE2 orthologs of nine Rhinolophus species enhanced human ACE2 binding to the SARS-CoV-2 RBD and neutralization of SARS-CoV-2 by an immunoadhesin form of human ACE2 (ACE2-Fc). Two of these mutations impaired neutralization of SARS-CoV-1. An ACE2-Fc variant bearing all five mutations neutralized SARS-CoV-2 five-fold more efficiently than human ACE2-Fc. These data narrow the potential SARS-CoV-2 reservoir, suggest that SARS-CoV-1 and -2 originate from distinct bat species, and identify a more potently neutralizing form of ACE2-Fc.
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Affiliation(s)
- Huihui Mou
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
- These authors contributed equally
| | - Brian D. Quinlan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
- These authors contributed equally
| | - Haiyong Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
- These authors contributed equally
| | - Yan Guo
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Shoujiao Peng
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Lizhou Zhang
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Matthew R. Gardner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Gogce Crynen
- Bioinformatics and Statistics Core, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Zhi Xiang Voo
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | | | - Christoph Rader
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Hyeryun Choe
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, FL 33458, USA
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21
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Park MS, Kim JI, Bae JY, Park MS. Animal models for the risk assessment of viral pandemic potential. Lab Anim Res 2020; 36:11. [PMID: 32337177 PMCID: PMC7175453 DOI: 10.1186/s42826-020-00040-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 03/10/2020] [Indexed: 02/07/2023] Open
Abstract
Pandemics affect human lives severely and globally. Experience predicts that there will be a pandemic for sure although the time is unknown. When a viral epidemic breaks out, assessing its pandemic risk is an important part of the process that characterizes genomic property, viral pathogenicity, transmission in animal model, and so forth. In this review, we intend to figure out how a pandemic may occur by looking into the past influenza pandemic events. We discuss interpretations of the experimental evidences resulted from animal model studies and extend implications of viral pandemic potentials and ingredients to emerging viral epidemics. Focusing on the pandemic potential of viral infectious diseases, we suggest what should be assessed to prevent global catastrophes from influenza virus, Middle East respiratory syndrome coronavirus, dengue and Zika viruses.
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Affiliation(s)
- Mee Sook Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Jin Il Kim
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Joon-Yong Bae
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
| | - Man-Seong Park
- Department of Microbiology, Institute for Viral Diseases, College of Medicine, Korea University, Seoul, Republic of Korea 02841
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22
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Chen YN, Hsu HC, Wang SW, Lien HC, Lu HT, Peng SK. Entry of Scotophilus Bat Coronavirus-512 and Severe Acute Respiratory Syndrome Coronavirus in Human and Multiple Animal Cells. Pathogens 2019; 8:pathogens8040259. [PMID: 31766704 PMCID: PMC6963420 DOI: 10.3390/pathogens8040259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/20/2019] [Accepted: 11/20/2019] [Indexed: 02/07/2023] Open
Abstract
Bats are natural reservoirs of severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome CoV (MERS-CoV). Scotophilus bat CoV-512 demonstrates potential for cross-species transmission because its viral RNA and specific antibodies have been detected in three bat species of Taiwan. Understanding the cell tropism of Scotophilus bat CoV-512 is the first step for studying the mechanism of cross-species transmission. In this study, a lentivirus-based pseudovirus was produced using the spike (S) protein of Scotophilus bat CoV-512 or SARS-CoV as a surface protein to test the interaction between coronaviral S protein and its cell receptor on 11 different cells. Susceptible cells expressed red fluorescence protein (RFP) after the entry of RFP-bound green fluorescence protein (GFP)-fused S protein of Scotophilus bat CoV-512 (RFP-Sco-S-eGFP) or RFP-SARS-S pseudovirus, and firefly luciferase (FLuc) activity expressed by cells infected with FLuc-Sco-S-eGFP or FLuc-SARS-S pseudovirus was quantified. Scotophilus bat CoV-512 pseudovirus had significantly higher entry efficiencies in Madin Darby dog kidney epithelial cells (MDCK), black flying fox brain cells (Pabr), and rat small intestine epithelial cells (IEC-6). SARS-CoV pseudovirus had significantly higher entry efficiencies in human embryonic kidney epithelial cells (HEK-293T), pig kidney epithelial cells (PK15), and MDCK cells. These findings demonstrated that Scotophilus bat CoV-512 had a broad host range for cross-species transmission like SARS-CoV.
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23
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Identification of a Novel Betacoronavirus ( Merbecovirus) in Amur Hedgehogs from China. Viruses 2019; 11:v11110980. [PMID: 31653070 PMCID: PMC6893546 DOI: 10.3390/v11110980] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Revised: 10/11/2019] [Accepted: 10/22/2019] [Indexed: 01/08/2023] Open
Abstract
While dromedaries are the immediate animal source of Middle East Respiratory Syndrome (MERS) epidemic, viruses related to MERS coronavirus (MERS-CoV) have also been found in bats as well as hedgehogs. To elucidate the evolution of MERS-CoV-related viruses and their interspecies transmission pathway, samples were collected from different mammals in China. A novel coronavirus related to MERS-CoV, Erinaceus amurensis hedgehog coronavirus HKU31 (Ea-HedCoV HKU31), was identified from two Amur hedgehogs. Genome analysis supported that Ea-HedCoV HKU31 represents a novel species under Merbecovirus, being most closely related to Erinaceus CoV from European hedgehogs in Germany, with 79.6% genome sequence identity. Compared to other members of Merbecovirus, Ea-HedCoV HKU31 possessed unique non-structural proteins and putative cleavage sites at ORF1ab. Phylogenetic analysis showed that Ea-HedCoV HKU31 and BetaCoV Erinaceus/VMC/DEU/2012 were closely related to NeoCoV and BatCoV PREDICT from African bats in the spike region, suggesting that the latter bat viruses have arisen from recombination between CoVs from hedgehogs and bats. The predicted HKU31 receptor-binding domain (RBD) possessed only one out of 12 critical amino acid residues for binding to human dipeptidyl peptidase 4 (hDPP4), the MERS-CoV receptor. The structural modeling of the HKU31-RBD-hDPP4 binding interphase compared to that of MERS-CoV and Tylonycteris bat CoV HKU4 (Ty-BatCoV HKU4) suggested that HKU31-RBD is unlikely to bind to hDPP4. Our findings support that hedgehogs are an important reservoir of Merbecovirus, with evidence of recombination with viruses from bats. Further investigations in bats, hedgehogs and related animals are warranted to understand the evolution of MERS-CoV-related viruses.
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Sawaswong V, Fahsbender E, Altan E, Kemthong T, Deng X, Malaivijitnond S, Payungporn S, Delwart E. High Diversity and Novel Enteric Viruses in Fecal Viromes of Healthy Wild and Captive Thai Cynomolgus Macaques ( Macaca fascicularis). Viruses 2019; 11:E971. [PMID: 31652508 PMCID: PMC6832579 DOI: 10.3390/v11100971] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 02/06/2023] Open
Abstract
Cynomolgus macaques are common across South East Asian countries including Thailand. The National Primate Research Center of Thailand, Chulalongkorn University (NPRCT-CU) captures wild-borne cynomolgus macaque for research use. Limited information is available on the enteric viruses and possible zoonotic infections into or from cynomolgus macaques. We characterized and compare the fecal virome of two populations; healthy wild-originated captive cynomolgus macaques (n = 43) reared in NPRCT-CU and healthy wild cynomolgus macaques (n = 35). Over 90% of recognized viral sequence reads amplified from feces were from bacterial viruses. Viruses from seven families of mammalian viruses were also detected (Parvoviridae, Anelloviridae, Picornaviridae, Adenoviridae, Papillomaviridae, Herpesviridae, and Caliciviridae). The genomes of a member of a new picornavirus genus we named Mafapivirus, a primate chapparvovirus, and a circular Rep-encoding single-strand (CRESS) DNA virus were also characterized. Higher abundance of CRESS DNA viruses of unknown tropism and invertebrate-tropic ambidensovirus were detected in wild versus captive macaques likely reflecting dietary differences. Short term rearing in captivity did not have a pronounced effect on the diversity of mammalian viruses of wild cynomolgus macaques. This study is the first report of the fecal virome of cynomolgus macaques, non-human primates frequently used in biomedical research and vaccination studies.
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Affiliation(s)
- Vorthon Sawaswong
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
| | - Elizabeth Fahsbender
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Eda Altan
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
| | - Taratorn Kemthong
- National Primate Research Center-Chulalongkorn University, Saraburi 18110, Thailand.
| | - Xutao Deng
- Vitalant Research Institute, San Francisco, CA 94118, USA.
| | | | - Sunchai Payungporn
- Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand.
- Center of Excellence in Systems Biology, Chulalongkorn University (CUSB), Bangkok 10330, Thailand.
| | - Eric Delwart
- Vitalant Research Institute, San Francisco, CA 94118, USA.
- Department of Laboratory Medicine, University of California San Francisco, San Francisco, CA 9413, USA.
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25
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Ramadan N, Shaib H. Middle East respiratory syndrome coronavirus (MERS-CoV): A review. Germs 2019; 9:35-42. [PMID: 31119115 DOI: 10.18683/germs.2019.1155] [Citation(s) in RCA: 156] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/08/2019] [Accepted: 01/26/2019] [Indexed: 12/31/2022]
Abstract
As a novel coronavirus first reported by Saudi Arabia in 2012, the Middle East respiratory syndrome coronavirus (MERS-CoV) is responsible for an acute human respiratory syndrome. The virus, of 2C beta-CoV lineage, expresses the dipeptidyl peptidase 4 (DPP4) receptor and is densely endemic in dromedary camels of East Africa and the Arabian Peninsula. MERS-CoV is zoonotic but human-to-human transmission is also possible. Surveillance and phylogenetic researches indicate MERS-CoV to be closely associated with bats' coronaviruses, suggesting bats as reservoirs, although unconfirmed. With no vaccine currently available for MERS-CoV nor approved prophylactics, its global spread to over 25 countries with high fatalities highlights its role as ongoing public health threat. An articulated action plan ought to be taken, preferably from a One Health perspective, for appropriately advanced countermeasures against MERS-CoV.
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Affiliation(s)
- Nour Ramadan
- MSc, Department of Agriculture, Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), Riad El Solh 1107-2020, PO Box 11-0236, Beirut, Lebanon
| | - Houssam Shaib
- PhD, Department of Agriculture, Faculty of Agricultural and Food Sciences (FAFS), American University of Beirut (AUB), Riad El Solh 1107-2020, PO Box 11-0236, Beirut, Lebanon
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26
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Wong ACP, Li X, Lau SKP, Woo PCY. Global Epidemiology of Bat Coronaviruses. Viruses 2019; 11:E174. [PMID: 30791586 PMCID: PMC6409556 DOI: 10.3390/v11020174] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Revised: 02/12/2019] [Accepted: 02/18/2019] [Indexed: 12/22/2022] Open
Abstract
Bats are a unique group of mammals of the order Chiroptera. They are highly diversified and are the group of mammals with the second largest number of species. Such highly diversified cell types and receptors facilitate them to be potential hosts of a large variety of viruses. Bats are the only group of mammals capable of sustained flight, which enables them to disseminate the viruses they harbor and enhance the chance of interspecies transmission. This article aims at reviewing the various aspects of the global epidemiology of bat coronaviruses (CoVs). Before the SARS epidemic, bats were not known to be hosts for CoVs. In the last 15 years, bats have been found to be hosts of >30 CoVs with complete genomes sequenced, and many more if those without genome sequences are included. Among the four CoV genera, only alphaCoVs and betaCoVs have been found in bats. As a whole, both alphaCoVs and betaCoVs have been detected from bats in Asia, Europe, Africa, North and South America and Australasia; but alphaCoVs seem to be more widespread than betaCoVs, and their detection rate is also higher. For betaCoVs, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus have been detected in bats. Most notably, horseshoe bats are the reservoir of SARS-CoV, and several betaCoVs from subgenus Merbecovirus are closely related to MERS-CoV. In addition to the interactions among various bat species themselves, bat⁻animal and bat⁻human interactions, such as the presence of live bats in wildlife wet markets and restaurants in Southern China, are important for interspecies transmission of CoVs and may lead to devastating global outbreaks.
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Affiliation(s)
- Antonio C P Wong
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Xin Li
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Susanna K P Lau
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
| | - Patrick C Y Woo
- Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
- State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
- Research Centre of Infection and Immunology, The University of Hong Kong, Pokfulam, Hong Kong.
- Carol Yu Centre for Infection, The University of Hong Kong, Pokfulam, Hong Kong.
- Collaborative Innovation Centre for Diagnosis and Treatment of Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong.
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27
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Interferon Regulatory Factor 3-Mediated Signaling Limits Middle-East Respiratory Syndrome (MERS) Coronavirus Propagation in Cells from an Insectivorous Bat. Viruses 2019; 11:v11020152. [PMID: 30781790 PMCID: PMC6410008 DOI: 10.3390/v11020152] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Revised: 02/08/2019] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
Insectivorous bats are speculated to be ancestral hosts of Middle-East respiratory syndrome (MERS) coronavirus (CoV). MERS-CoV causes disease in humans with thirty-five percent fatality, and has evolved proteins that counteract human antiviral responses. Since bats experimentally infected with MERS-CoV do not develop signs of disease, we tested the hypothesis that MERS-CoV would replicate less efficiently in bat cells than in human cells because of its inability to subvert antiviral responses in bat cells. We infected human and bat (Eptesicus fuscus) cells with MERS-CoV and observed that the virus grew to higher titers in human cells. MERS-CoV also effectively suppressed the antiviral interferon beta (IFNβ) response in human cells, unlike in bat cells. To determine if IRF3, a critical mediator of the interferon response, also regulated the response in bats, we examined the response of IRF3 to poly(I:C), a synthetic analogue of viral double-stranded RNA. We observed that bat IRF3 responded to poly(I:C) by nuclear translocation and post-translational modifications, hallmarks of IRF3 activation. Suppression of IRF3 by small-interfering RNA (siRNA) demonstrated that IRF3 was critical for poly(I:C) and MERS-CoV induced induction of IFNβ in bat cells. Our study demonstrates that innate antiviral signaling in E. fuscus bat cells is resistant to MERS-CoV-mediated subversion.
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28
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Bats and Coronaviruses. Viruses 2019; 11:v11010041. [PMID: 30634396 PMCID: PMC6356540 DOI: 10.3390/v11010041] [Citation(s) in RCA: 266] [Impact Index Per Article: 53.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/05/2019] [Accepted: 01/07/2019] [Indexed: 11/17/2022] Open
Abstract
Bats are speculated to be reservoirs of several emerging viruses including coronaviruses (CoVs) that cause serious disease in humans and agricultural animals. These include CoVs that cause severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), porcine epidemic diarrhea (PED) and severe acute diarrhea syndrome (SADS). Bats that are naturally infected or experimentally infected do not demonstrate clinical signs of disease. These observations have allowed researchers to speculate that bats are the likely reservoirs or ancestral hosts for several CoVs. In this review, we follow the CoV outbreaks that are speculated to have originated in bats. We review studies that have allowed researchers to identify unique adaptation in bats that may allow them to harbor CoVs without severe disease. We speculate about future studies that are critical to identify how bats can harbor multiple strains of CoVs and factors that enable these viruses to “jump” from bats to other mammals. We hope that this review will enable readers to identify gaps in knowledge that currently exist and initiate a dialogue amongst bat researchers to share resources to overcome present limitations.
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