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Shi J, Hu S, Wei H, Zhang L, Lan Y, Guan J, Zhao K, Gao F, He W, Li Z. Dipeptidyl peptidase 4 interacts with porcine coronavirus PHEV spikes and mediates host range expansion. J Virol 2024:e0075324. [PMID: 38829136 DOI: 10.1128/jvi.00753-24] [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: 04/29/2024] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Porcine hemagglutinating encephalomyelitis virus (PHEV), a neurotropic betacoronavirus, is prevalent in natural reservoir pigs and infects mice. This raises concerns about host jumping or spillover, but little is known about the cause of occurrence. Here, we revealed that dipeptidyl peptidase 4 (DPP4) is a candidate binding target of PHEV spikes and works as a broad barrier to overcome. Investigations of the host breadth of PHEV confirmed that cells derived from pigs and mice are permissive to virus propagation. Both porcine DPP4 and murine DPP4 have high affinity for the viral spike receptor-binding domain (RBD), independent of their catalytic activity. Loss of DPP4 expression results in limited PHEV infection. Structurally, PHEV spike protein binds to the outer surface of blades IV and V of the DPP4 β-propeller domain, and the DPP4 residues N229 and N321 (relative to human DPP4 numbering) participate in RBD binding via its linked carbohydrate entities. Removal of these N-glycosylations profoundly enhanced the RBD-DPP4 interaction and viral invasion, suggesting they act as shielding in PHEV infection. Furthermore, we found that glycosylation, rather than structural differences or surface charges, is more responsible for DPP4 recognition and species barrier formation. Overall, our findings shed light on virus-receptor interactions and highlight that PHEV tolerance to DPP4 orthologs is a putative determinant of its cross-species transmission or host range expansion.IMPORTANCEPHEV is a neurotropic betacoronavirus that is circulating worldwide and has raised veterinary and economic concerns. In addition to being a reservoir species of pigs, PHEV can also infect wild-type mice, suggesting a "host jump" event. Understanding cross-species transmission is crucial for disease prevention and control but remains to be addressed. Herein, we show that the multifunctional receptor DPP4 plays a pivotal role in the host tropism of PHEV and identifies the conserved glycosylation sites in DPP4 responsible for this restriction. These findings highlight that the ability of PHEV to utilize DPP4 orthologs potentially affects its natural host expansion.
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Affiliation(s)
- Junchao Shi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
- Key Laboratory of Organ Regeneration and Transplantation of the Ministry of Education, Jilin University, Changchun, China
| | - Shiyu Hu
- Department of Immunology, School of Basic Medical Sciences, Beijing Key Laboratory of Tumor Systems Biology, Institute of Systems Biomedicine, Peking University Health Science Center, Beijing, China
| | - Hanlu Wei
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Le Zhang
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Yungang Lan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Jiyu Guan
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Kui Zhao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Feng Gao
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Wenqi He
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
| | - Zi Li
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, and College of Veterinary Medicine, Jilin University, Changchun, China
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Isibor PO, Onwaeze OO, Kayode-Edwards II, Agbontaen DO, Ifebem-Ezima IAM, Bilewu O, Onuselogu C, Akinniyi AP, Obafemi YD, Oniha MI. Investigating and combatting the key drivers of viral zoonoses in Africa: an analysis of eight epidemics. BRAZ J BIOL 2023; 84:e270857. [PMID: 37531478 DOI: 10.1590/1519-6984.270857] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/02/2023] [Indexed: 08/04/2023] Open
Abstract
Investigating the interplay of factors that result in a viral zoonotic outbreak is difficult, though it is increasingly important. As anthropogenic influences shift the delicate balance of ecosystems, new zoonoses emerge in humans. Sub-Saharan Africa is a notable hotspot for zoonotic disease due to abundant competent mammalian reservoir hosts. Furthermore, poverty, corruption, and an overreliance on natural resources play considerable roles in depleting biological resources, exacerbating the population's susceptibility. Unsurprisingly, viral zoonoses have emerged in Africa, including HIV/AIDS, Ebola, Avian influenza, Lassa fever, Zika, and Monkeypox. These diseases are among the principal causes of death in endemic areas. Though typically distinct in their manifestations, viral zoonoses are connected by underlying, definitive factors. This review summarises vital findings on viral zoonoses in Africa using nine notable case studies as a benchmark for future studies. We discuss the importance of ecological recuperation and protection as a central strategy to control zoonotic diseases. Emphasis was made on moderating key drivers of zoonotic diseases to forestall future pandemics. This is in conjunction with attempts to redirect efforts from reactive to pre-emptive through a multidisciplinary "one health" approach.
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Affiliation(s)
- P O Isibor
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O O Onwaeze
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - I I Kayode-Edwards
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - D O Agbontaen
- University of South Wales, Department of Public Health, Pontypridd, United Kingdom
| | - I-A M Ifebem-Ezima
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - O Bilewu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - C Onuselogu
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - A P Akinniyi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - Y D Obafemi
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
| | - M I Oniha
- Covenant University, Department of Biological Sciences, Ota, Ogun State, Nigeria
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3
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Cao L, Li Y, Yang S, Li G, Zhou Q, Sun J, Xu T, Yang Y, Liao R, Shi Y, Yang Y, Zhu T, Huang S, Ji Y, Cong F, Luo Y, Zhu Y, Luan H, Zhang H, Chen J, Liu X, Luo R, Liu L, Wang P, Yu Y, Xing F, Ke B, Zheng H, Deng X, Zhang W, Lin C, Shi M, Li CM, Zhang Y, Zhang L, Dai J, Lu H, Zhao J, Zhang X, Guo D. The adenosine analog prodrug ATV006 is orally bioavailable and has preclinical efficacy against parental SARS-CoV-2 and variants. Sci Transl Med 2022; 14:eabm7621. [PMID: 35579533 PMCID: PMC9161374 DOI: 10.1126/scitranslmed.abm7621] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus driving the ongoing coronavirus disease 2019 (COVID-19) pandemic, continues to rapidly evolve. Due to the limited efficacy of vaccination in prevention of SARS-CoV-2 transmission and continuous emergence of variants of concern (VOC), orally bioavailable and broadly efficacious antiviral drugs are urgently needed. Previously we showed that the parent nucleoside of remdesivir, GS-441524, possesses potent anti-SARS-CoV-2 activity. Herein, we report that esterification of the 5′-hydroxyl moieties of GS-441524 markedly improved antiviral potency. This 5′-hydroxyl-isobutyryl prodrug, ATV006, demonstrated excellent oral bioavailability in rats and cynomolgus monkeys and exhibited potent antiviral efficacy against different SARS-CoV-2 VOCs in vitro and in three mouse models. Oral administration of ATV006 reduced viral loads and alleviated lung damage when administered prophylactically and therapeutically to K18-hACE2 mice challenged with the Delta variant of SARS-CoV-2. These data indicate that ATV006 represents a promising oral antiviral drug candidate for SARS-CoV-2.
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Affiliation(s)
- Liu Cao
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Yingjun Li
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Sidi Yang
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Guanguan Li
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong 518118, China
| | - Qifan Zhou
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Jing Sun
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China
| | - Tiefeng Xu
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Yang Yang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for infectious disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Ruyan Liao
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong 510623, China
| | - Yongxia Shi
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong 510623, China
| | - Yujian Yang
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Tiaozhen Zhu
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Siyao Huang
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Yanxi Ji
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Feng Cong
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong 510663, China
| | - Yinzhu Luo
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong 510663, China
| | - Yujun Zhu
- Guangdong Province Key Laboratory of Laboratory Animals, Guangdong Laboratory Animals Monitoring Institute, Guangzhou, Guangdong 510663, China
| | - Hemi Luan
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Huan Zhang
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, Guangdong 511430, China
| | - Jingdiao Chen
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, Guangdong 511430, China
| | - Xue Liu
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Renru Luo
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Lihong Liu
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Ping Wang
- Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong 518118, China
| | - Yang Yu
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Fan Xing
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Bixia Ke
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, Guangdong 511430, China
| | - Huanying Zheng
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, Guangdong 511430, China
| | - Xiaoling Deng
- Center for Disease Control and Prevention of Guangdong Province, Guangzhou, Guangdong 511430, China
| | - Wenyong Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China
| | - Chuwen Lin
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Mang Shi
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Chun-Mei Li
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
| | - Yu Zhang
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong 510623, China
| | - Lu Zhang
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for infectious disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Jun Dai
- Guangzhou Customs District Technology Center, Guangzhou, Guangdong 510623, China
| | - Hongzhou Lu
- Shenzhen Key Laboratory of Pathogen and Immunity, National Clinical Research Center for infectious disease, State Key Discipline of Infectious Disease, Shenzhen Third People's Hospital, Second Hospital Affiliated to Southern University of Science and Technology, Shenzhen, Guangdong 518112, China
| | - Jincun Zhao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong 510182, China.,Guangzhou Laboratory, Bio-island, Guangzhou, Guangdong 510320, People's Republic of China
| | - Xumu Zhang
- Shenzhen Key Laboratory of Small Molecule Drug Discovery and Synthesis, Department of Chemistry, College of Science, Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, Guangdong 518055, China.,Medi-X Pingshan, Southern University of Science and Technology, Shenzhen, Guangdong 518118, China
| | - Deyin Guo
- Centre for Infection and Immunity Studies (CIIS), School of Medicine, Shenzhen Campus of Sun Yat-sen University, Guangdong 518107, China
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4
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Gyebi GA, Adegunloye AP, Ibrahim IM, Ogunyemi OM, Afolabi SO, Ogunro OB. Prevention of SARS-CoV-2 cell entry: insight from in silico interaction of drug-like alkaloids with spike glycoprotein, human ACE2, and TMPRSS2. J Biomol Struct Dyn 2022; 40:2121-2145. [PMID: 33089728 PMCID: PMC7594191 DOI: 10.1080/07391102.2020.1835726] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 10/07/2020] [Indexed: 12/28/2022]
Abstract
COVID-19 is a respiratory disease caused by SARS-CoV-2, an enveloped positive sense RNA virus. The SARS-CoV-2 spike glycoprotein, human angiotensin-converting enzyme 2 (ACE2) and human transmembrane protease serine 2 (TMPRSS2) are essential for the host cell-mediated viral entry. Targeting these proteins represent viable options to stop the first stage of infection and transmission. Hence, 97 alkaloids from African medicinal plants with reported antiviral activity were evaluated for this purpose via in silico studies. These alkaloids were docked for their interactions with SARS-CoV-2 spike glycoprotein, ACE2, and TMPRSS2. Top 20 alkaloids with highest binding affinities were further screened for their interactions with spike glycoprotein of SARS-CoV and MERS-CoV, and with ACE2-SARS-CoV-2 receptor-binding domain complex (ACE2-RBD). The energy profiling, molecular dynamics simulation (MDS), binding free energy base on Molecular Mechanics/Generalized Born Surface Area (MMGBSA), clustering of MDS trajectories, and virtual physicochemical and pharmacokinetic screening of the best docked alkaloids were performed. Results revealed that more than 15 alkaloids interacted better than the reference compounds. 10-Hydroxyusambarensine and Cryptospirolepine were docked in a similar binding pattern to the S1-specificy pocket of TMPRSS2 as camostat (reference inhibitor). The strong binding affinities, stability of the alkaloid-protein complexes and amino acid interactions displayed by cryptospirolepine, 10-hydroxyusambarensine, and cryptoquindoline with important binding hotspots of the proteins suggest these alkaloids have the potential of altering the capacity of SARS-CoV-2 membrane mediated host cell entry. Further in vitro and in vivo evaluation of these "drug-like" alkaloids as potential inhibitors of coronavirus cell entry is proposed.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Gideon A. Gyebi
- Department of Biological Sciences, Salem University, Lokoja, Nigeria
| | | | - Ibrahim M. Ibrahim
- Faculty of Sciences, Department of Biophysics, Cairo University, Giza, Egypt
| | | | - Saheed O. Afolabi
- Faculty of Basic Medical Sciences, Department of Pharmacology and Therapeutics, University of Ilorin, Ilorin, Nigeria
| | - Olalekan B. Ogunro
- Department of Biological Sciences, KolaDaisi University, Ibadan, Nigeria
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Zhang D, Yang Y, Li M, Lu Y, Liu Y, Jiang J, Liu R, Liu J, Huang X, Li G, Qu J. Ecological Barrier Deterioration Driven by Human Activities Poses Fatal Threats to Public Health due to Emerging Infectious Diseases. ENGINEERING (BEIJING, CHINA) 2022; 10:155-166. [PMID: 33903827 PMCID: PMC8060651 DOI: 10.1016/j.eng.2020.11.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/26/2020] [Accepted: 11/10/2020] [Indexed: 05/24/2023]
Abstract
The coronavirus disease 2019 (COVID-19) and concerns about several other pandemics in the 21st century have attracted extensive global attention. These emerging infectious diseases threaten global public health and raise urgent studies on unraveling the underlying mechanisms of their transmission from animals to humans. Although numerous works have intensively discussed the cross-species and endemic barriers to the occurrence and spread of emerging infectious diseases, both types of barriers play synergistic roles in wildlife habitats. Thus far, there is still a lack of a complete understanding of viral diffusion, migration, and transmission in ecosystems from a macro perspective. In this review, we conceptualize the ecological barrier that represents the combined effects of cross-species and endemic barriers for either the natural or intermediate hosts of viruses. We comprehensively discuss the key influential factors affecting the ecological barrier against viral transmission from virus hosts in their natural habitats into human society, including transmission routes, contact probability, contact frequency, and viral characteristics. Considering the significant impacts of human activities and global industrialization on the strength of the ecological barrier, ecological barrier deterioration driven by human activities is critically analyzed for potential mechanisms. Global climate change can trigger and expand the range of emerging infectious diseases, and human disturbances promote higher contact frequency and greater transmission possibility. In addition, globalization drives more transmission routes and produces new high-risk regions in city areas. This review aims to provide a new concept for and comprehensive evidence of the ecological barrier blocking the transmission and spread of emerging infectious diseases. It also offers new insights into potential strategies to protect the ecological barrier and reduce the wide-ranging risks of emerging infectious diseases to public health.
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Affiliation(s)
- Dayi Zhang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yunfeng Yang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Miao Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yun Lu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Yi Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jingkun Jiang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Ruiping Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jianguo Liu
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Xia Huang
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Guanghe Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Jiuhui Qu
- School of Environment, Tsinghua University, Beijing 100084, China
- Key Laboratory of Drinking Water Science and Technology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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Khan J, Asoom LIA, Khan M, Chakrabartty I, Dandoti S, Rudrapal M, Zothantluanga JH. Evolution of RNA viruses from SARS to SARS-CoV-2 and diagnostic techniques for COVID-19: a review. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2021; 10:60. [PMID: 34642633 PMCID: PMC8494164 DOI: 10.1186/s43088-021-00150-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 09/20/2021] [Indexed: 01/12/2023] Open
Abstract
Background From the start of the twenty-first century up to the year 2021, RNA viruses are the main causative agents of the majority of the disease outbreaks the world has confronted. Recently published reviews on SARS-CoV-2 have mainly focused on its structure, development of the outbreak, relevant precautions, management trials and available therapies. However, in this review, we aim to explore the history, evolution of all coronaviruses and the associated viral outbreaks along with the diagnostics for COVID-19 in the twenty-first century.
Main body We have focused on different RNA viruses’ viz. SARS-CoV, MERS-CoV, and SARS-CoV-2, their classification, and the various disease outbreaks caused by them. In the subsequent section, the comparison of different RNA viruses affecting humans has been made based on the viral genome, structure, time of the outbreak, mode of spread, virulence, causative agents, and transmission. Due to the current mayhem caused by the rapidly emerging virus, special attention is given to SARS-CoV-2, its genome updates, and infectivity. Finally, the current diagnostic techniques such as nucleic acid testing (real time-polymerase chain reaction and loop-mediated isothermal amplification), CRISPR-based diagnostics (CRISPR based DETECTR assay, CRISPR based SHERLOCK test, AIOD-CRISPR, FELUDA, CREST), chest radiographs (computed tomography, X-ray), and serological tests (Lateral flow assay, enzyme-linked immunosorbent assay, chemiluminescent immunoassay, neutralization assay, nano-sensors, blood test, viral sequencing) with their pros and cons, and future diagnostic prospective have been described.
Conclusions The present gloomy scenario mandates clinical manifestations, contact tracing, and laboratory tests as important parameters that need to be taken into consideration to make the final diagnosis.
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Affiliation(s)
- Johra Khan
- Department of Medical Laboratory Sciences, College of Applied Medical Sciences, Majmaah University, Majmaah, 11952 Saudi Arabia
| | - Lubna Ibrahim Al Asoom
- Physiology Department, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Maryam Khan
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, Uttar Pradesh 202002 India
| | - Ishani Chakrabartty
- Department of Science, P.A. First Grade College (Affiliated To Mangalore University, Mangalore), Nadupadav, Mangalore, Karnataka 574153 India
| | - Sayequa Dandoti
- Department of Biology, Deanship of Preparatory Year, Imam Abdulrahman Bin Faisal University, Dammam, 31541 Saudi Arabia
| | - Mithun Rudrapal
- Department of Pharmaceutical Chemistry, Rasiklal M. Dhariwal Institute of Pharmaceutical Education & Research (Affiliated to Savitribai Phule Pune University, Pune) , Chinchwad, Pune, Maharashtra 411019 India
| | - James H Zothantluanga
- Department of Pharmaceutical Sciences, Faculty of Science and Engineering, Dibrugarh University, Dibrugarh, Assam 786004 India
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de Vries RD, Rockx B, Haagmans BL, Herfst S, Koopmans MP, de Swart RL. Animal models of SARS-CoV-2 transmission. Curr Opin Virol 2021; 50:8-16. [PMID: 34256352 PMCID: PMC8238653 DOI: 10.1016/j.coviro.2021.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 02/06/2023]
Abstract
SARS-CoV-2 emerged in China as a zoonotic virus in December 2019. The virus proved to be human-to-human transmissible and its global spread resulted in the ongoing COVID-19 pandemic, associated with high morbidity and mortality. Vaccines were developed at an unprecedented speed and proved to be efficacious in preventing disease, but it remains to be determined if vaccines are able to interrupt transmission. Moreover, virus variants of concern continue to emerge that appear more transmissible and/or less sensitive to virus-specific immune responses. Here, we briefly review the role of animal models in assessing prophylactic and therapeutic options to interrupt SARS-CoV-2 transmission.
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Affiliation(s)
- Rory D de Vries
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Barry Rockx
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Bart L Haagmans
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Sander Herfst
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Marion Pg Koopmans
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Rik L de Swart
- Department Viroscience, Erasmus MC, University Medical Center Rotterdam, The Netherlands.
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Jia P, Dai S, Wu T, Yang S. New Approaches to Anticipate the Risk of Reverse Zoonosis. Trends Ecol Evol 2021; 36:580-590. [PMID: 33966919 PMCID: PMC8100872 DOI: 10.1016/j.tree.2021.03.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 03/23/2021] [Accepted: 03/31/2021] [Indexed: 12/30/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic can cause reverse zoonoses (i.e., human-animal transmission of COVID-19). It is vital to utilize up-to-date methods to improve the control, management, and prevention of reverse zoonoses. Awareness of reverse zoonoses should be raised at both individual and regional/national levels for better protection of both humans and animals.
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Affiliation(s)
- Peng Jia
- School of Resources and Environmental Science, Wuhan University, Wuhan, China; Department of Land Surveying and Geo-Informatics, The Hong Kong Polytechnic University, Hong Kong, China; International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China.
| | - Shaoqing Dai
- International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
| | - Tong Wu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
| | - Shujuan Yang
- West China School of Public Health and West China Fourth Hospital, Sichuan University, Chengdu, China; International Institute of Spatial Lifecourse Epidemiology (ISLE), Hong Kong, China
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9
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Mondal S, Karmakar A, Mallick T, Begum NA. Exploring the efficacy of naturally occurring biflavone based antioxidants towards the inhibition of the SARS-CoV-2 spike glycoprotein mediated membrane fusion. Virology 2021; 556:133-139. [PMID: 33571798 PMCID: PMC7860945 DOI: 10.1016/j.virol.2021.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/22/2022]
Abstract
Molecular docking studies were done to show the inhibitory effect of two naturally occurring biflavone based anti-HIV agents, hinokiflavone and robustaflavone against the SARS-CoV-2 spike (S) protein mediated attack on the human ACE2 receptors via membrane fusion mechanism. Nefamostat, a FDA approved drug, well-known as a serine protease inhibitor for MERS-CoV infection, was used as the reference compound. Both the biflavones, showed potential as inhibitors for SARS-CoV-2 S protein-mediated viral entry. The binding affinities of these naturally occurring biflavones for RBD-S2 subunit protein of SARS-CoV-2 were explored for the first time. Such binding affinities play a critical role in the virus-cell membrane fusion process. These biflavones are able to interact more strongly with the residues of heptad repeat 1 and 2 (HR1 and HR2) regions of S2 protein of SARS-CoV-2 compared to nefamostat, and thus, these biflavones can effectively block the formation of six-helix bundle core fusion structure (6-HB) leading to the inhibition of virus-target cell-membrane fusion.
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Affiliation(s)
- Samiran Mondal
- Department of Chemistry, Rammohan College, 102/1-Raja Rammohan Sarani, Kolkata, 700009, West Bengal, India.
| | - Abhijit Karmakar
- Department of Chemistry, Visva-Bharati (Central University), Santiniketan, 731 235, India
| | - Tamanna Mallick
- Department of Chemistry, Visva-Bharati (Central University), Santiniketan, 731 235, India
| | - Naznin Ara Begum
- Department of Chemistry, Visva-Bharati (Central University), Santiniketan, 731 235, India
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10
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Lesimple A, Jasim SY, Johnson DJ, Hilal N. The role of wastewater treatment plants as tools for SARS-CoV-2 early detection and removal. JOURNAL OF WATER PROCESS ENGINEERING 2020; 38:101544. [PMID: 38620686 PMCID: PMC7377730 DOI: 10.1016/j.jwpe.2020.101544] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 05/03/2023]
Abstract
The world is facing the third coronavirus caused pandemic in less than twenty years. The SARS-CoV-2 virus not only affects the human respiratory system, but also the gastrointestinal tract. The virus has been found in human feces, in sewage and in wastewater treatment plants. It has the potential to become a panzootic disease, as it is now proven that several mammalian species become infected. Since it has been shown that the virus can be detected in sewage even before the onset of symptoms in the local population, Wastewater Based Epidemiology should be developed not only to localize infection clusters of the primary wave but also to detect a potential second, or subsequent, wave. To prevent a panzootic, virus removal techniques from wastewater need to be implemented to prevent the virus dissemination into the environment. In that context, this review presents recent improvements in all the fields of wastewater treatment from treatment ponds to the use of algae or nanomaterials with a particular emphasis on membrane-based techniques.
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Affiliation(s)
- Alain Lesimple
- NYUAD Water Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
| | - Saad Y Jasim
- SJ Environmental Consultants (Windsor) Inc., 4483 Cherry Hill Road, Windsor, Ontario, N9G 2W3 Canada
| | - Daniel J Johnson
- Centre for Water Advanced Technologies and Environmental Research (CWATER), College of Engineering, Swansea University, Fabian Way, Swansea SA1 8EN, United Kingdom
| | - Nidal Hilal
- NYUAD Water Research Center, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates
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11
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Mechanistic insights of host cell fusion of SARS-CoV-1 and SARS-CoV-2 from atomic resolution structure and membrane dynamics. Biophys Chem 2020; 265:106438. [PMID: 32721790 PMCID: PMC7375304 DOI: 10.1016/j.bpc.2020.106438] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 07/16/2020] [Accepted: 07/17/2020] [Indexed: 01/04/2023]
Abstract
The emerging and re-emerging viral diseases are continuous threats to the wellbeing of human life. Previous outbreaks of Severe Acute Respiratory Syndrome (SARS) and Middle East Respiratory Syndrome (MERS had evidenced potential threats of coronaviruses in human health. The recent pandemic due to SARS-CoV-2 is overwhelming and has been going beyond control. Vaccines and antiviral drugs are ungently required to mitigate the pandemic. Therefore, it is important to comprehend the mechanistic details of viral infection process. The fusion between host cell and virus being the first step of infection, understanding the fusion mechanism could provide crucial information to intervene the infection process. Interestingly, all enveloped viruses contain fusion protein on their envelope that acts as fusion machine. For coronaviruses, the spike or S glycoprotein mediates successful infection through receptor binding and cell fusion. The cell fusion process requires merging of virus and host cell membranes, and that is essentially performed by the S2 domain of the S glycoprotein. In this review, we have discussed cell fusion mechanism of SARS-CoV-1 from available atomic resolution structures and membrane binding of fusion peptides. We have further discussed about the cell fusion of SARS-CoV-2 in the context of present pandemic situation.
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12
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Otto DP, de Villiers MM. Layer-By-Layer Nanocoating of Antiviral Polysaccharides on Surfaces to Prevent Coronavirus Infections. Molecules 2020; 25:E3415. [PMID: 32731428 PMCID: PMC7435837 DOI: 10.3390/molecules25153415] [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] [Received: 07/10/2020] [Revised: 07/24/2020] [Accepted: 07/26/2020] [Indexed: 12/28/2022] Open
Abstract
In 2020, the world is being ravaged by the coronavirus, SARS-CoV-2, which causes a severe respiratory disease, Covid-19. Hundreds of thousands of people have succumbed to the disease. Efforts at curing the disease are aimed at finding a vaccine and/or developing antiviral drugs. Despite these efforts, the WHO warned that the virus might never be eradicated. Countries around the world have instated non-pharmaceutical interventions such as social distancing and wearing of masks in public to curb the spreading of the disease. Antiviral polysaccharides provide the ideal opportunity to combat the pathogen via pharmacotherapeutic applications. However, a layer-by-layer nanocoating approach is also envisioned to coat surfaces to which humans are exposed that could harbor pathogenic coronaviruses. By coating masks, clothing, and work surfaces in wet markets among others, these antiviral polysaccharides can ensure passive prevention of the spreading of the virus. It poses a so-called "eradicate-in-place" measure against the virus. Antiviral polysaccharides also provide a green chemistry pathway to virus eradication since these molecules are primarily of biological origin and can be modified by minimal synthetic approaches. They are biocompatible as well as biodegradable. This surface passivation approach could provide a powerful measure against the spreading of coronaviruses.
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Affiliation(s)
- Daniel P. Otto
- Research Focus Area for Chemical Resource Beneficiation, Laboratory for Analytical Services, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2531, South Africa
| | - Melgardt M. de Villiers
- Division of Pharmaceutical Sciences–Drug Delivery, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Ave, Madison, WI 53705, USA;
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13
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Genomic Sequencing and Analysis of Eight Camel-Derived Middle East Respiratory Syndrome Coronavirus (MERS-CoV) Isolates in Saudi Arabia. Viruses 2020; 12:v12060611. [PMID: 32503352 PMCID: PMC7354450 DOI: 10.3390/v12060611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 12/25/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory illness in humans; the second-largest and most deadly outbreak to date occurred in Saudi Arabia. The dromedary camel is considered a possible host of the virus and also to act as a reservoir, transmitting the virus to humans. Here, we studied evolutionary relationships for 31 complete genomes of betacoronaviruses, including eight newly sequenced MERS-CoV genomes isolated from dromedary camels in Saudi Arabia. Through bioinformatics tools, we also used available sequences and 3D structure of MERS-CoV spike glycoprotein to predict MERS-CoV epitopes and assess antibody binding affinity. Phylogenetic analysis showed the eight new sequences have close relationships with existing strains detected in camels and humans in Arabian Gulf countries. The 2019-nCov strain appears to have higher homology to both bat coronavirus and SARS-CoV than to MERS-CoV strains. The spike protein tree exhibited clustering of MERS-CoV sequences similar to the complete genome tree, except for one sequence from Qatar (KF961222). B cell epitope analysis determined that the MERS-CoV spike protein has 24 total discontinuous regions from which just six epitopes were selected with score values of >80%. Our results suggest that the virus circulates by way of camels crossing the borders of Arabian Gulf countries. This study contributes to finding more effective vaccines in order to provide long-term protection against MERS-CoV and identifying neutralizing antibodies.
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14
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Rong TMD, Nina LMD, Ping LMD, Qi TMD, Qizhi YMD. Comparative Study of CT Characteristics in Imported Cases and Indigenous Cases with COVID-19. ADVANCED ULTRASOUND IN DIAGNOSIS AND THERAPY 2020. [DOI: 10.37015/audt.2020.200016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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15
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Ababneh M, Alrwashdeh M, Khalifeh M. Recombinant adenoviral vaccine encoding the spike 1 subunit of the Middle East Respiratory Syndrome Coronavirus elicits strong humoral and cellular immune responses in mice. Vet World 2019; 12:1554-1562. [PMID: 31849416 PMCID: PMC6868266 DOI: 10.14202/vetworld.2019.1554-1562] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Accepted: 08/26/2019] [Indexed: 01/05/2023] Open
Abstract
Background and Aim Middle East respiratory syndrome coronavirus (MERS-CoV) has rapidly spread throughout the Middle East since its discovery in 2012. The virus poses a significant global public health threat with potentially devastating effects. In this study, a recombinant adenoviral-based vaccine encoding the spike 1 (S1) subunit of the MERS-CoV genome was constructed, and its humoral, and cellular immune responses were evaluated in mice. Materials and Methods Mice were immunized initially by intramuscular injection and boosted 3 weeks later by intranasal application. Expression of the S1 protein in the lungs and kidneys was detected using conventional polymerase chain reaction (PCR) and immunohistochemistry (IHC) targeting specific regions within the S1 subunit at weeks 3, 4, 5, and 6 after the first vaccination. Antigen-specific humoral and cellular immune responses were evaluated in serum and in cell culture following in vitro stimulation with a specific 9-mer epitope within the S1 protein (CYSSLILDY). Results S1 protein expression was only detected by IHC in the kidneys of the Ad-MERS-S1 group at week 6 from first immunization, and in both lungs and kidneys of Ad-MERS-S1 group by conventional PCR at weeks 3 and 5 post-prime. The vaccine elicited a specific S1-immunoglobulin G antibody response, which was detected in the sera of the vaccinated mice at weeks 4 and 6 from the onset of the first immunization. There was a significant increase in the amount of Th1-related cytokines (interferon-γ and interleukin [IL] 12), and a significant decrease in the Th2-related cytokine IL-4 in splenocyte cell culture of the vaccinated group compared with the control groups. Conclusion The results of this study suggest that this recombinant adenovirus vaccine encoding the S1 subunit of MERS-CoV elicits potentially protective antigen-specific humoral and cellular immune responses in mice. This study demonstrates a promising vaccine for the control and/or prevention of MERS-CoV infection in humans.
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Affiliation(s)
- Mustafa Ababneh
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Mu'men Alrwashdeh
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
| | - Mohammad Khalifeh
- Department of Basic Medical Veterinary Sciences, Jordan University of Science and Technology, P.O. Box 3030, Irbid 22110, Jordan
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16
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Cheng Y, He B, Yang J, Ye F, Lin S, Yang F, Chen Z, Chen Z, Cao Y, Lu G. Crystal structure of the S1 subunit N-terminal domain from DcCoV UAE-HKU23 spike protein. Virology 2019; 535:74-82. [PMID: 31279241 PMCID: PMC7112003 DOI: 10.1016/j.virol.2019.06.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 06/18/2019] [Accepted: 06/26/2019] [Indexed: 02/05/2023]
Abstract
The DcCoV UAE-HKU23 coronavirus is a newly-found betacoronavirus (betaCoV) that can infect human cells. The viral spike protein plays pivotal roles in mediating receptor-recognition and membrane-fusion, and is therefore a key factor involved in viral pathogenesis and inter-species transmission. Here we reported the structural and functional characterization of the spike N-terminal domain (NTD) from DcCoV UAE-HKU23 (HKU23-NTD). Via mucin-binding assays, we showed that HKU23-NTD is able to bind sugars. We further solved the structure of HKU23-NTD, performed structure-guided mutagenesis and successfully located the potential sugar-binding pockets in the structure. Furthermore, via comparison of available betaCoV NTD structures, we demonstrated that betaCoV NTDs contain a conserved β-sandwich core, but exhibit variant folds in the peripheral elements located in the top-ceiling region and on the lateral side. While showing different compositions and structures, these peripheral elements are topologically equivalent β-sandwich-core insertions, highlighting a divergent evolution process for betaCoVs to form different lineages.
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Affiliation(s)
- Yanwei Cheng
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Bin He
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China
| | - Jing Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Fei Ye
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Sheng Lin
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Fanli Yang
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Zimin Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Zhujun Chen
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Yu Cao
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China,Corresponding author. West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China
| | - Guangwen Lu
- West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China,Corresponding author
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17
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Serological Screening for Coronavirus Infections in Cats. Viruses 2019; 11:v11080743. [PMID: 31412572 PMCID: PMC6723642 DOI: 10.3390/v11080743] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 12/21/2022] Open
Abstract
Coronaviruses (CoVs) are widespread among mammals and birds and known for their potential for cross-species transmission. In cats, infections with feline coronaviruses (FCoVs) are common. Several non-feline coronaviruses have been reported to infect feline cells as well as cats after experimental infection, supported by their ability to engage the feline receptor ortholog for cell entry. However, whether cats might become naturally infected with CoVs of other species is unknown. We analyzed coronavirus infections in cats by serological monitoring. In total 137 cat serum samples and 25 FCoV type 1 or type 2-specific antisera were screened for the presence of antibodies against the S1 receptor binding subunit of the CoV spike protein, which is immunogenic and possesses low amino acid sequence identity among coronavirus species. Seventy-eight sera were positive for antibodies that recognized one or more coronavirus S1s whereas 1 serum exclusively reacted with human coronavirus 229E (HCoV-229E) and two sera exclusively reacted with porcine delta coronavirus (PDCoV). We observed antigenic cross-reactivity between S1s of type 1 and type 2 FCoVs, and between FCoV type 1 and porcine epidemic diarrhea virus (PEDV). Domain mapping of antibody epitopes indicated the presence of conserved epitope(s) particularly in the CD domains of S1. The cross-reactivity of FCoV type 1 and PEDV was also observed at the level of virus neutralization. To conclude, we provide the first evidence of antigenic cross-reactivity among S1 proteins of coronaviruses, which should be considered in the development of serological diagnoses. In addition, the potential role of cats in cross-species transmission of coronaviruses cannot be excluded.
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18
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Zhu S, Zimmerman D, Deem SL. A Review of Zoonotic Pathogens of Dromedary Camels. ECOHEALTH 2019; 16:356-377. [PMID: 31140075 PMCID: PMC7087575 DOI: 10.1007/s10393-019-01413-7] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 03/12/2019] [Accepted: 03/12/2019] [Indexed: 06/09/2023]
Abstract
Dromedary, or one-humped, camels Camelus dromedarius are an almost exclusively domesticated species that are common in arid areas as both beasts of burden and production animals for meat and milk. Currently, there are approximately 30 million dromedary camels, with highest numbers in Africa and the Middle East. The hardiness of camels in arid regions has made humans more dependent on them, especially as a stable protein source. Camels also carry and may transmit disease-causing agents to humans and other animals. The ability for camels to act as a point source or vector for disease is a concern due to increasing human demands for meat, lack of biosafety and biosecurity protocols in many regions, and a growth in the interface with wildlife as camel herds become sympatric with non-domestic species. We conducted a literature review of camel-borne zoonotic diseases and found that the majority of publications (65%) focused on Middle East respiratory syndrome (MERS), brucellosis, Echinococcus granulosus, and Rift Valley fever. The high fatality from MERS outbreaks during 2012-2016 elicited an immediate response from the research community as demonstrated by a surge of MERS-related publications. However, we contend that other camel-borne diseases such as Yersinia pestis, Coxiella burnetii, and Crimean-Congo hemorrhagic fever are just as important to include in surveillance efforts. Camel populations, particularly in sub-Saharan Africa, are increasing exponentially in response to prolonged droughts, and thus, the risk of zoonoses increases as well. In this review, we provide an overview of the major zoonotic diseases present in dromedary camels, their risk to humans, and recommendations to minimize spillover events.
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Affiliation(s)
- Sophie Zhu
- Graduate Group in Epidemiology, University of California, Davis, CA, 95616, USA.
| | - Dawn Zimmerman
- Global Health Program, Smithsonian Conservation Biology Institute, Washington, DC, 20008, USA
| | - Sharon L Deem
- Institute for Conservation Medicine, Saint Louis Zoo, Saint Louis, MO, 63110, USA
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19
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Saberi A, Gulyaeva AA, Brubacher JL, Newmark PA, Gorbalenya AE. A planarian nidovirus expands the limits of RNA genome size. PLoS Pathog 2018; 14:e1007314. [PMID: 30383829 PMCID: PMC6211748 DOI: 10.1371/journal.ppat.1007314] [Citation(s) in RCA: 86] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 09/02/2018] [Indexed: 12/28/2022] Open
Abstract
RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication (albeit within a permissive host environment). A 33.5 kilobase (kb) nidovirus has been considered close to the upper size limit for such entities; conversely, the minimal cellular DNA genome is in the 100–300 kb range. This large difference presents a daunting gap for the transition from primordial RNP to contemporary DNA-RNP-based life. Whether or not RNA viruses represent transitional steps towards DNA-based life, studies of larger RNA viruses advance our understanding of the size constraints on RNP entities and the role of genome size in virus adaptation. For example, emergence of the largest previously known RNA genomes (20–34 kb in positive-stranded nidoviruses, including coronaviruses) is associated with the acquisition of a proofreading exoribonuclease (ExoN) encoded in the open reading frame 1b (ORF1b) in a monophyletic subset of nidoviruses. However, apparent constraints on the size of ORF1b, which encodes this and other key replicative enzymes, have been hypothesized to limit further expansion of these viral RNA genomes. Here, we characterize a novel nidovirus (planarian secretory cell nidovirus; PSCNV) whose disproportionately large ORF1b-like region including unannotated domains, and overall 41.1-kb genome, substantially extend the presumed limits on RNA genome size. This genome encodes a predicted 13,556-aa polyprotein in an unconventional single ORF, yet retains canonical nidoviral genome organization and expression, as well as key replicative domains. These domains may include functionally relevant substitutions rarely or never before observed in highly conserved sites of RdRp, NiRAN, ExoN and 3CLpro. Our evolutionary analysis suggests that PSCNV diverged early from multi-ORF nidoviruses, and acquired additional genes, including those typical of large DNA viruses or hosts, e.g. Ankyrin and Fibronectin type II, which might modulate virus-host interactions. PSCNV's greatly expanded genome, proteomic complexity, and unique features–impressive in themselves–attest to the likelihood of still-larger RNA genomes awaiting discovery. RNA viruses are the only known RNA-protein (RNP) entities capable of autonomous replication. The upper genome size for such entities was assumed to be <35 kb; conversely, the minimal cellular DNA genome is in the 100–300 kilobase (kb) range. This large difference presents a daunting gap for the proposed evolution of contemporary DNA-RNP-based life from primordial RNP entities. Here, we describe a nidovirus from planarians, named planarian secretory cell nidovirus (PSCNV), whose 41.1 kb genome is 23% larger than any riboviral genome yet discovered. This increase is nearly equivalent in size to the entire poliovirus genome, and it equips PSCNV with an unprecedented extra coding capacity to adapt. PSCNV has broken apparent constraints on the size of the genomic subregion that encodes core replication machinery in other nidoviruses, including coronaviruses, and has acquired genes not previously observed in RNA viruses. This virus challenges and advances our understanding of the limits to RNA genome size.
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Affiliation(s)
- Amir Saberi
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
| | - Anastasia A. Gulyaeva
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - John L. Brubacher
- Department of Biology, Canadian Mennonite University, Winnipeg, Canada
| | - Phillip A. Newmark
- Howard Hughes Medical Institute, Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States of America
- * E-mail: (PAN); (AEG)
| | - Alexander E. Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia
- * E-mail: (PAN); (AEG)
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Comparison of Perceived and Observed Hand Hygiene Compliance in Healthcare Workers in MERS-CoV Endemic Regions. Healthcare (Basel) 2018; 6:healthcare6040122. [PMID: 30301272 PMCID: PMC6315729 DOI: 10.3390/healthcare6040122] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/17/2022] Open
Abstract
This study investigated healthcare workers’ perceptions of hand hygiene practices by comparing personal reports, as assessed by questionnaires, to direct observations of the workers’ hand hygiene practices. The study employed a cross-sectional research design. Observations were made using a 16-item checklist, based on three sources: Centers for Disease Control and Prevention (CDC), World Health Organization (WHO), and Boyce and Pittet’s guidelines of hand hygiene. The checklist was used for both direct-observation and self-reported data collection purposes. Pearson correlation and Multivariate Analysis of Covariance (MANCOVA) were utilized to statistically determine the relationship between healthcare workers’ reports of hand hygiene practices and observed hand hygiene behaviors. The study was conducted in the outpatient examination rooms and emergency departments of three types of hospitals in the Eastern region of Saudi Arabia where Middle East respiratory syndrome coronavirus (MERS-CoV) is endemic and is observed in routine cases and outbreaks. The total sample size included 87 physicians and nurses recruited while on duty during the scheduled observation periods, with each healthcare worker being observed during individual medical examinations with at least three patients. No statistically significant correlations between the healthcare workers’ perceptions of hand hygiene practices and healthcare workers’ actual behaviors were evident. Based on the self-report questionnaires, significant differences were found between physicians’ and nurses’ hand hygiene practices reports. Healthcare workers clearly understand the importance of careful hand hygiene practices, but based on researchers’ observations, the medical personnel failed to properly implement protocol-driven hand hygiene applications. However, the significant differences between physicians’ and nurses’ self-reports suggest further inquiry is needed to fully explore these discrepancies.
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21
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Alfaraj SH, Al-Tawfiq JA, Gautret P, Alenazi MG, Asiri AY, Memish ZA. Evaluation of visual triage for screening of Middle East respiratory syndrome coronavirus patients. New Microbes New Infect 2018; 26:49-52. [PMID: 30224971 PMCID: PMC6138856 DOI: 10.1016/j.nmni.2018.08.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/07/2018] [Accepted: 08/03/2018] [Indexed: 12/22/2022] Open
Abstract
The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in September 2012 in Saudi Arabia had attracted the attention of the global health community. In 2017 the Saudi Ministry of Health released a visual triage system with scoring to alert healthcare workers in emergency departments (EDs) and haemodialysis units for the possibility of occurrence of MERS-CoV infection. We performed a retrospective analysis of this visual score to determine its sensitivity and specificity. The study included all cases from 2014 to 2017 in a MERS-CoV referral centre in Riyadh, Saudi Arabia. During the study period there were a total of 2435 suspected MERS cases. Of these, 1823 (75%) tested negative and the remaining 25% tested positive for MERS-CoV by PCR assay. The application of the visual triage score found a similar percentage of MERS-CoV and non–MERS-CoV patients, with each score from 0 to 11. The percentage of patients with a cutoff score of ≥4 was 75% in patients with MERS-CoV infection and 85% in patients without MERS-CoV infection (p 0.0001). The sensitivity and specificity of this cutoff score for MERS-CoV infection were 74.1% and 18.6%, respectively. The sensitivity and specificity of the scoring system were low, and further refinement of the score is needed for better prediction of MERS-CoV infection.
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Affiliation(s)
- S H Alfaraj
- Corona Center, Infectious Diseases Division, Department of Pediatrics, Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Saudi Arabia.,University of British Columbia, Vancouver, Canada
| | - J A Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Indiana University School of Medicine, Indianapolis, IN, USA.,Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - P Gautret
- Aix-Marseille Université, Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) UM63 CNRS 7278 IRD 198 INSERM U1095, Marseille, France
| | - M G Alenazi
- Pediatric Emergency Medicine, Emergency Department, Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Saudi Arabia
| | - A Y Asiri
- Critical Care Department, Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Saudi Arabia
| | - Z A Memish
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.,Infectious Diseases Division, Department of Medicine, Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Saudi Arabia
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22
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Alfaraj SH, Al-Tawfiq JA, Altuwaijri TA, Memish ZA. Middle East respiratory syndrome coronavirus in pediatrics: a report of seven cases from Saudi Arabia. Front Med 2018; 13:126-130. [PMID: 29623560 PMCID: PMC7088593 DOI: 10.1007/s11684-017-0603-y] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 10/23/2017] [Indexed: 01/12/2023]
Abstract
Infection with Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012 as an important respiratory disease with high fatality rates of 40%-60%. Despite the increased number of cases over subsequent years, the number of pediatric cases remained low. A review of studies conducted from June 2012 to April 19, 2016 reported 31 pediatric MERS-CoV cases. In this paper, we present the clinical and laboratory features of seven patients with pediatric MERS. Five patients had no underlying medical illnesses, and three patients were asymptomatic. Of the seven cases, four (57%) patients sought medical advice within 1-7 days from the onset of symptoms. The three other patients (43%) were asymptomatic and were in contact with patients with confirmed diagnosis of MERS-CoV. The most common presenting symptoms were fever (57%), cough (14%), shortness of breath (14%), vomiting (28%), and diarrhea (28%). Two (28.6%) patients had platelet counts of < 150 × 109/L, and one patient had an underlying end-stage renal disease. The remaining patients presented with normal blood count, liver function, and urea and creatinine levels. The documented MERS-CoV Ct values were 32-38 for four of the seven cases. Two patients (28.6%) had abnormal chest radiographic findings of bilateral infiltration. One patient (14.3%) required ventilator support, and two patients (28.6%) required oxygen supplementation. All the seven patients were discharged without complications.
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Affiliation(s)
- Sarah H Alfaraj
- University of British Columbia, Vancouver, V6T 1Z4, Canada.,Corona Center, Infectious Diseases Division, Department of Pediatric, Prince Mohamed Bin Abdulaziz Hospital, Ministry of Health, Riyadh, 11676, Saudi Arabia
| | - Jaffar A Al-Tawfiq
- Indiana University School of Medicine, Indianapolis, IN, 46202, USA.,Johns Hopkins Aramco Healthcare, Dhahran, 31311, Saudi Arabia
| | - Talal A Altuwaijri
- Department of Surgery, King Saud University, Riyadh, 11692, Saudi Arabia
| | - Ziad A Memish
- College of Medicine, Alfaisal University, Riyadh, 11533, Saudi Arabia. .,Infectious Diseases Division, Department of Medicine, Prince Mohamed Bin Abdulaziz Hospital, Ministry of Health, Riyadh, 11676, Saudi Arabia. .,Hubert Department of Global Health, Rollins School of Public Health, Emory University, Atlanta, GA, 30322, USA.
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23
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Cho H, Excler JL, Kim JH, Yoon IK. Development of Middle East Respiratory Syndrome Coronavirus vaccines - advances and challenges. Hum Vaccin Immunother 2017; 14:304-313. [PMID: 29048984 DOI: 10.1080/21645515.2017.1389362] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is an emerging pathogen with the potential to pose a threat to global public health. Sporadic cases and outbreaks continue to be reported in the Middle East, and case fatality rates remain high at approximately 36% globally. No specific preventive or therapeutic countermeasures currently exist. A safe and effective vaccine could play an important role in protecting against the threat from MERS-CoV. This review discusses human vaccine candidates currently under development, and explores viral characteristics, molecular epidemiology and immunology relevant to MERS-CoV vaccine development. At present, a DNA vaccine candidate has begun a human clinical trial, while two vector-based candidates will very soon begin human trials. Protein-based vaccines are still at pre-clinical stage. Challenges to successful development include incomplete understanding of viral transmission, pathogenesis and immune response (in particular at the mucosal level), no optimal animal challenge models, lack of standardized immunological assays, and insufficient sustainable funding.
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Affiliation(s)
- Heeyoun Cho
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - Jean-Louis Excler
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - Jerome H Kim
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
| | - In-Kyu Yoon
- a Department of Clinical Development and Regulatory , International Vaccine Institute , Seoul , Republic of Korea
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24
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Dietert K, Gutbier B, Wienhold SM, Reppe K, Jiang X, Yao L, Chaput C, Naujoks J, Brack M, Kupke A, Peteranderl C, Becker S, von Lachner C, Baal N, Slevogt H, Hocke AC, Witzenrath M, Opitz B, Herold S, Hackstein H, Sander LE, Suttorp N, Gruber AD. Spectrum of pathogen- and model-specific histopathologies in mouse models of acute pneumonia. PLoS One 2017; 12:e0188251. [PMID: 29155867 PMCID: PMC5695780 DOI: 10.1371/journal.pone.0188251] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/05/2017] [Indexed: 01/03/2023] Open
Abstract
Pneumonia may be caused by a wide range of pathogens and is considered the most common infectious cause of death in humans. Murine acute lung infection models mirror human pathologies in many aspects and contribute to our understanding of the disease and the development of novel treatment strategies. Despite progress in other fields of tissue imaging, histopathology remains the most conclusive and practical read out tool for the descriptive and semiquantitative evaluation of mouse pneumonia and therapeutic interventions. Here, we systematically describe and compare the distinctive histopathological features of established models of acute pneumonia in mice induced by Streptococcus (S.) pneumoniae, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Legionella pneumophila, Escherichia coli, Middle East respiratory syndrome (MERS) coronavirus, influenza A virus (IAV) and superinfection of IAV-incuced pneumonia with S. pneumoniae. Systematic comparisons of the models revealed striking differences in the distribution of lesions, the characteristics of pneumonia induced, principal inflammatory cell types, lesions in adjacent tissues, and the detectability of the pathogens in histological sections. We therefore identified core criteria for each model suitable for practical semiquantitative scoring systems that take into account the pathogen- and model-specific patterns of pneumonia. Other critical factors that affect experimental pathologies are discussed, including infectious dose, time kinetics, and the genetic background of the mouse strain. The substantial differences between the model-specific pathologies underscore the necessity of pathogen- and model-adapted criteria for the comparative quantification of experimental outcomes. These criteria also allow for the standardized validation and comparison of treatment strategies in preclinical models.
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MESH Headings
- Acinetobacter baumannii/pathogenicity
- Acinetobacter baumannii/physiology
- Animals
- Disease Models, Animal
- Escherichia coli/pathogenicity
- Escherichia coli/physiology
- Female
- Host Specificity
- Humans
- Immunohistochemistry
- Influenza A virus/pathogenicity
- Influenza A virus/physiology
- Klebsiella pneumoniae/pathogenicity
- Klebsiella pneumoniae/physiology
- Legionella pneumophila/pathogenicity
- Legionella pneumophila/physiology
- Lung/microbiology
- Lung/pathology
- Lung/virology
- Mice
- Mice, Inbred BALB C
- Mice, Inbred C57BL
- Middle East Respiratory Syndrome Coronavirus/pathogenicity
- Middle East Respiratory Syndrome Coronavirus/physiology
- Pneumonia, Bacterial/genetics
- Pneumonia, Bacterial/microbiology
- Pneumonia, Bacterial/pathology
- Pneumonia, Bacterial/physiopathology
- Pneumonia, Viral/genetics
- Pneumonia, Viral/pathology
- Pneumonia, Viral/physiopathology
- Pneumonia, Viral/virology
- Species Specificity
- Staphylococcus aureus/pathogenicity
- Staphylococcus aureus/physiology
- Streptococcus pneumoniae/pathogenicity
- Streptococcus pneumoniae/physiology
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Affiliation(s)
- Kristina Dietert
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
| | - Birgitt Gutbier
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra M. Wienhold
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Katrin Reppe
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Xiaohui Jiang
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Ling Yao
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Catherine Chaput
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Jan Naujoks
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Markus Brack
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Alexandra Kupke
- Department of Internal Medicine II, Section for Infectious Diseases, Universities Giessen & Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) Giessen, Germany
- Institute of Virology, Philipps University of Marburg, German Center for Infection Research (DZIF), TTU Emerging Infections, Marburg, Germany
| | - Christin Peteranderl
- Department of Internal Medicine II, Section for Infectious Diseases, Universities Giessen & Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) Giessen, Germany
| | - Stephan Becker
- Department of Internal Medicine II, Section for Infectious Diseases, Universities Giessen & Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) Giessen, Germany
- Institute of Virology, Philipps University of Marburg, German Center for Infection Research (DZIF), TTU Emerging Infections, Marburg, Germany
| | | | - Nelli Baal
- Institute for Clinical Immunology and Transfusion Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), University Hospital Giessen und Marburg, Justus-Liebig-University Giessen, Giessen, Germany
| | - Hortense Slevogt
- Septomics Research Center, Jena University Hospital, Jena, Germany
| | - Andreas C. Hocke
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Martin Witzenrath
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Bastian Opitz
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Susanne Herold
- Department of Internal Medicine II, Section for Infectious Diseases, Universities Giessen & Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL) Giessen, Germany
| | - Holger Hackstein
- Institute for Clinical Immunology and Transfusion Medicine, Universities of Giessen and Marburg Lung Center (UGMLC), Member of the German Center for Lung Research (DZL), University Hospital Giessen und Marburg, Justus-Liebig-University Giessen, Giessen, Germany
| | - Leif E. Sander
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Norbert Suttorp
- Department of Infectious Diseases and Pulmonary Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Achim D. Gruber
- Department of Veterinary Pathology, Freie Universität Berlin, Berlin, Germany
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25
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Mahajan M, Chatterjee D, Bhuvaneswari K, Pillay S, Bhattacharjya S. NMR structure and localization of a large fragment of the SARS-CoV fusion protein: Implications in viral cell fusion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:407-415. [PMID: 28988778 PMCID: PMC7094225 DOI: 10.1016/j.bbamem.2017.10.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 09/16/2017] [Accepted: 10/03/2017] [Indexed: 01/20/2023]
Abstract
The lethal Coronaviruses (CoVs), Severe Acute Respiratory Syndrome-associated Coronavirus (SARS-CoV) and most recently Middle East Respiratory Syndrome Coronavirus, (MERS-CoV) are serious human health hazard. A successful viral infection requires fusion between virus and host cells carried out by the surface spike glycoprotein or S protein of CoV. Current models propose that the S2 subunit of S protein assembled into a hexameric helical bundle exposing hydrophobic fusogenic peptides or fusion peptides (FPs) for membrane insertion. The N-terminus of S2 subunit of SARS-CoV reported to be active in cell fusion whereby FPs have been identified. Atomic-resolution structure of FPs derived either in model membranes or in membrane mimic environment would glean insights toward viral cell fusion mechanism. Here, we have solved 3D structure, dynamics and micelle localization of a 64-residue long fusion peptide or LFP in DPC detergent micelles by NMR methods. Micelle bound structure of LFP is elucidated by the presence of discretely folded helical and intervening loops. The C-terminus region, residues F42-Y62, displays a long hydrophobic helix, whereas the N-terminus is defined by a short amphipathic helix, residues R4-Q12. The intervening residues of LFP assume stretches of loops and helical turns. The N-terminal helix is sustained by close aromatic and aliphatic sidechain packing interactions at the non-polar face. 15N{1H}NOE studies indicated dynamical motion, at ps-ns timescale, of the helices of LFP in DPC micelles. PRE NMR showed that insertion of several regions of LFP into DPC micelle core. Together, the current study provides insights toward fusion mechanism of SARS-CoV.
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Affiliation(s)
- Mukesh Mahajan
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Deepak Chatterjee
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Kannaian Bhuvaneswari
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Shubhadra Pillay
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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26
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Al-Tawfiq JA, Hinedi K, Abbasi S, Babiker M, Sunji A, Eltigani M. Hematologic, hepatic, and renal function changes in hospitalized patients with Middle East respiratory syndrome coronavirus. Int J Lab Hematol 2017; 39:272-278. [PMID: 28444873 PMCID: PMC7165514 DOI: 10.1111/ijlh.12620] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 11/21/2016] [Indexed: 12/24/2022]
Abstract
Background There are no longitudinal data on the changes in hematologic, hepatic, and renal function findings in patients with Middle East respiratory syndrome coronavirus (MERS‐CoV) infection. Methods This is a retrospective cohort study of 16 MERS‐CoV patients, to describe the hematological, hepatic, and renal findings of patients with MERS‐CoV. Results During the 21 days of observation, there was no significant change in the hepatic panel or creatinine tests. There was a significant increase in the mean ± SD of the white blood cell count from 8.3 ± 4.6 to 14.53 ± 7 (P value = 0.001) and an increase in mean ± SD of the absolute neutrophil count from 6.33 ± 4.2 to 12 ± 5.5 (P value = 0.015). Leukocytosis was observed in 31% (5/16) of the patients on day 1 and in 80% (4/5) on day 21. Transient leukopenia developed in 6% (1/16) of the patients on day 1 and in 13% (1/8) on day 8. None of the patients had neutropenia. Lymphopenia was a prominent feature with a rate of 44% (7/16) of the patients on day 1 and 60% (3/5) on day 21. Lymphocytosis was not a feature of MERS‐CoV infection. Thrombocytopenia developed in 31% (5/16) of the patients on day 1 and 40% (2/5) on day 21. Thrombocytosis was not a prominent feature and was observed in 6% (1/16) of the patients on day 1 and 17% (1/6) on day 9. Conclusions Patients with MERS‐CoV infection showed variable hematologic parameters over time. Lymphocytosis and neutropenia were not features of MERS‐CoV infection.
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Affiliation(s)
- J A Al-Tawfiq
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia.,Indiana University School of Medicine, Indianapolis, Indiana, USA
| | - K Hinedi
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - S Abbasi
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - M Babiker
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - A Sunji
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
| | - M Eltigani
- Internal Medicine, Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia
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27
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Cryo-EM structures of MERS-CoV and SARS-CoV spike glycoproteins reveal the dynamic receptor binding domains. Nat Commun 2017; 8:15092. [PMID: 28393837 PMCID: PMC5394239 DOI: 10.1038/ncomms15092] [Citation(s) in RCA: 541] [Impact Index Per Article: 77.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Accepted: 02/24/2017] [Indexed: 02/05/2023] Open
Abstract
The envelope spike (S) proteins of MERS-CoV and SARS-CoV determine the virus host tropism and entry into host cells, and constitute a promising target for the development of prophylactics and therapeutics. Here, we present high-resolution structures of the trimeric MERS-CoV and SARS-CoV S proteins in its pre-fusion conformation by single particle cryo-electron microscopy. The overall structures resemble that from other coronaviruses including HKU1, MHV and NL63 reported recently, with the exception of the receptor binding domain (RBD). We captured two states of the RBD with receptor binding region either buried (lying state) or exposed (standing state), demonstrating an inherently flexible RBD readily recognized by the receptor. Further sequence conservation analysis of six human-infecting coronaviruses revealed that the fusion peptide, HR1 region and the central helix are potential targets for eliciting broadly neutralizing antibodies. Host tropism and cell entry of pathogenic coronaviruses are mediated by their envelope spike (S) proteins. Here the authors present structural analyses of trimeric MERS-CoV and SARS-CoV S proteins in pre-fusion conformation, and reveal two states of the receptor binding domain that suggest new avenues for the generation of neutralizing antibodies.
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28
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Miguel E, Chevalier V, Ayelet G, Ben Bencheikh MN, Boussini H, Chu DK, El Berbri I, Fassi-Fihri O, Faye B, Fekadu G, Grosbois V, Ng BC, Perera RA, So TY, Traore A, Roger F, Peiris M. Risk factors for MERS coronavirus infection in dromedary camels in Burkina Faso, Ethiopia, and Morocco, 2015. Euro Surveill 2017; 22:30498. [PMID: 28382915 PMCID: PMC5388105 DOI: 10.2807/1560-7917.es.2017.22.13.30498] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 02/03/2017] [Indexed: 11/20/2022] Open
Abstract
Understanding Middle East respiratory syndrome coronavirus (MERS-CoV) transmission in dromedary camels is important, as they consitute a source of zoonotic infection to humans. To identify risk factors for MERS-CoV infection in camels bred in diverse conditions in Burkina Faso, Ethiopia and Morocco, blood samples and nasal swabs were sampled in February-March 2015. A relatively high MERS-CoV RNA rate was detected in Ethiopia (up to 15.7%; 95% confidence interval (CI): 8.2-28.0), followed by Burkina Faso (up to 12.2%; 95% CI: 7-20.4) and Morocco (up to 7.6%; 95% CI: 1.9-26.1). The RNA detection rate was higher in camels bred for milk or meat than in camels for transport (p = 0.01) as well as in younger camels (p = 0.06). High seropositivity rates (up to 100%; 95% CI: 100-100 and 99.4%; 95% CI: 95.4-99.9) were found in Morocco and Ethiopia, followed by Burkina Faso (up to 84.6%; 95% CI: 77.2-89.9). Seropositivity rates were higher in large/medium herds (≥51 camels) than small herds (p = 0.061), in camels raised for meat or milk than for transport (p = 0.01), and in nomadic or sedentary herds than in herds with a mix of these lifestyles (p < 0.005).
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Affiliation(s)
- Eve Miguel
- Cirad UPR AGIRs, Montpellier, France
- UMR CNRS, IRD, UM, 5290 MIVEGEC, Montpellier, France
| | | | | | | | | | - Daniel Kw Chu
- School of Public Health, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | | | | | | | | | | | - Bryan Cy Ng
- School of Public Health, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - Ranawaka Apm Perera
- School of Public Health, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | - T Y So
- School of Public Health, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
| | | | | | - Malik Peiris
- School of Public Health, The University of Hong Kong, Hong Kong Special Adminstrative Region, China
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29
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Abstract
Middle East Respiratory Syndrome coronavirus (MERS-CoV) emerged in 2012 has since resulted in sporadic cases, intra-familial transmission and major outbreaks in healthcare settings. The clinical picture of MERS-CoV includes asymptomatic infections, mild or moderately symptomatic cases and fatal disease. Transmissions of MERS-CoV within healthcare settings are facilitated by overcrowding, poor compliance with basic infection control measures, unrecognized infections, the superspreaders phenomenon and poor triage systems. The actual contributing factors to the spread of MERS-CoV are yet to be systematically studied, but data to date suggest viral, host and environmental factors play a major role. Here, we summarize the known factors for the diverse transmission of MERS-CoV.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- a Medical Department , Johns Hopkins Aramco Healthcare , Dhahran , Saudi Arabia.,b Department of Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Ziad A Memish
- c Medical Department , Ministry of Health , Riyadh , Kingdom of Saudi Arabia.,d College of Medicine , Alfaisal University , Riyadh , Kingdom of Saudi Arabia
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30
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Funk AL, Goutard FL, Miguel E, Bourgarel M, Chevalier V, Faye B, Peiris JSM, Van Kerkhove MD, Roger FL. MERS-CoV at the Animal-Human Interface: Inputs on Exposure Pathways from an Expert-Opinion Elicitation. Front Vet Sci 2016; 3:88. [PMID: 27761437 PMCID: PMC5051548 DOI: 10.3389/fvets.2016.00088] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 09/14/2016] [Indexed: 12/30/2022] Open
Abstract
Nearly 4 years after the first report of the emergence of Middle-East respiratory syndrome Coronavirus (MERS-CoV) and nearly 1800 human cases later, the ecology of MERS-CoV, its epidemiology, and more than risk factors of MERS-CoV transmission between camels are poorly understood. Knowledge about the pathways and mechanisms of transmission from animals to humans is limited; as of yet, transmission risks have not been quantified. Moreover the divergent sanitary situations and exposures to animals among populations in the Arabian Peninsula, where human primary cases appear to dominate, vs. other regions in the Middle East and Africa, with no reported human clinical cases and where the virus has been detected only in dromedaries, represents huge scientific and health challenges. Here, we have used expert-opinion elicitation in order to obtain ideas on relative importance of MERS-CoV risk factors and estimates of transmission risks from various types of contact between humans and dromedaries. Fourteen experts with diverse and extensive experience in MERS-CoV relevant fields were enrolled and completed an online questionnaire that examined pathways based on several scenarios, e.g., camels-camels, camels-human, bats/other species to camels/humans, and the role of diverse biological substances (milk, urine, etc.) and potential fomites. Experts believed that dromedary camels play the largest role in MERS-CoV infection of other dromedaries; however, they also indicated a significant influence of the season (i.e. calving or weaning periods) on transmission risk. All experts thought that MERS-CoV-infected dromedaries and asymptomatic humans play the most important role in infection of humans, with bats and other species presenting a possible, but yet undefined, risk. Direct and indirect contact of humans with dromedary camels were identified as the most risky types of contact, when compared to consumption of various camel products, with estimated "most likely" incidence risks of at least 22 and 13% for direct and indirect contact, respectively. The results of our study are consistent with available, yet very limited, published data regarding the potential pathways of transmission of MERS-CoV at the animal-human interface. These results identify key knowledge gaps and highlight the need for more comprehensive, yet focused research to be conducted to better understand transmission between dromedaries and humans.
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Affiliation(s)
| | | | - Eve Miguel
- Cirad, UPR AGIRs Research Unit, Montpellier, France; UMR MIVEGEC, IRD 224-CNRS 5290-UM, Montpellier, France
| | | | | | - Bernard Faye
- Cirad, UPR AGIRs Research Unit , Montpellier , France
| | - J S Malik Peiris
- HKU-Pasteur Research Pole, Hong Kong, China; School of Public Health, University of Hong Kong, Hong Kong, China
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31
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Min J, Cella E, Ciccozzi M, Pelosi A, Salemi M, Prosperi M. The global spread of Middle East respiratory syndrome: an analysis fusing traditional epidemiological tracing and molecular phylodynamics. Glob Health Res Policy 2016; 1:14. [PMID: 29202063 PMCID: PMC5693564 DOI: 10.1186/s41256-016-0014-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/14/2016] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Since its discovery in 2012, over 1700 confirmed cases of Middle East Respiratory Syndrome (MERS) have been documented worldwide and more than a third of those cases have died. While the greatest number of cases has occurred in Saudi Arabia, the recent export of MERS-coronavirus (MERS-CoV) to Republic of Korea showed that a pandemic is a possibility that cannot be ignored. Due to the deficit of knowledge in transmission methodology, targeted treatment and possible vaccines, understanding this virus should be a priority. Our aim was to combine epidemiological data from literature with genetic information from viruses sequenced around the world to present a phylodynamic picture of MERS spread molecular level to global scale. METHODS We performed a qualitative meta-analysis of all laboratory confirmed cases worldwide to date based on literature, with emphasis on international transmission and healthcare associated infections. In parallel, we used publicly available MERS-CoV genomes from GenBank to create a phylogeographic tree, detailing geospatial timeline of viral evolution. RESULTS Several healthcare associated outbreaks starting with the retrospectively identified hospital outbreak in Jordan to the most recent outbreak in Riyadh, Saudi Arabia have occurred. MERS has also crossed many oceans, entering multiple nations in eight waves between 2012 and 2015. In this paper, the spatiotemporal history of MERS cases, as documented epidemiologically, was examined by Bayesian phylogenetic analysis. Distribution of sequences into geographic clusters and interleaving of MERS-CoV sequences from camels among those isolated from humans indicated that multiple zoonotic introductions occurred in endemic nations. We also report a summary of basic reproduction numbers for MERS-CoV in humans and camels. CONCLUSION Together, these analyses can help us identify factors associated with viral evolution and spread as well as establish efficacy of infection control measures. The results are especially pertinent to countries without current MERS-CoV endemic, since their unfamiliarity makes them particularly susceptible to uncontrollable spread of a virus that may be imported by travelers.
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Affiliation(s)
- Jae Min
- Department of Epidemiology, College of Public Health & Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL 32610-0231 USA
| | - Eleonora Cella
- Department of Infectious, Parasitic and Immune-mediated Diseases, National Institute of Health, Viale Regina Elena, 299, 00161 Rome, Italy
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro, 5, 00185 Rome, Italy
- Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, Gainesville, FL 32611 USA
| | - Massimo Ciccozzi
- Department of Infectious, Parasitic and Immune-mediated Diseases, National Institute of Health, Viale Regina Elena, 299, 00161 Rome, Italy
- Department of Clinical Pathology and Microbiology Laboratory, University of Biomedical Campus, Via Alvaro del Portillo, 21, Rome, Italy
| | - Antonello Pelosi
- Department of Infectious, Parasitic and Immune-mediated Diseases, National Institute of Health, Viale Regina Elena, 299, 00161 Rome, Italy
| | - Marco Salemi
- Department of Pathology, Immunology and Laboratory Medicine, Emerging Pathogens Institute, University of Florida, 2055 Mowry Rd, Gainesville, FL 32611 USA
| | - Mattia Prosperi
- Department of Epidemiology, College of Public Health & Health Professions and College of Medicine, University of Florida, 2004 Mowry Rd, Gainesville, FL 32610-0231 USA
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Al-Tawfiq JA, Omrani AS, Memish ZA. Middle East respiratory syndrome coronavirus: current situation and travel-associated concerns. Front Med 2016; 10:111-9. [PMID: 27146399 PMCID: PMC7089395 DOI: 10.1007/s11684-016-0446-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 03/21/2016] [Indexed: 01/05/2023]
Abstract
The emergence of Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 brought back memories of the occurrence of severe acute respiratory syndrome coronavirus (SARS-CoV) in 2002. More than 1500 MERS-CoV cases were recorded in 42 months with a case fatality rate (CFR) of 40%. Meanwhile, 8000 cases of SARS-CoV were confirmed in six months with a CFR of 10%. The clinical presentation of MERS-CoV ranges from mild and non-specific presentation to progressive and severe pneumonia. No predictive signs or symptoms exist to differentiate MERS-CoV from community-acquired pneumonia in hospitalized patients. An apparent heterogeneity was observed in transmission. Most MERS-CoV cases were secondary to large outbreaks in healthcare settings. These cases were secondary to community-acquired cases, which may also cause family outbreaks. Travel-associated MERS infection remains low. However, the virus exhibited a clear tendency to cause large outbreaks outside the Arabian Peninsula as exemplified by the outbreak in the Republic of Korea. In this review, we summarize the current knowledge about MERS-CoV and highlight travel-related issues.
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Affiliation(s)
- Jaffar A Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran, 31311, Kingdom of Saudi Arabia.,Indiana University School of Medicine, Indianapolis, IN, 46202-3082, USA
| | - Ali S Omrani
- Department of Medicine, Section of Infectious Diseases, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Ziad A Memish
- Ministry of Health, Riyadh, 11514, Kingdom of Saudi Arabia. .,College of Medicine, Alfaisal University, Riyadh, 11533, Kingdom of Saudi Arabia.
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Weber DJ, Rutala WA, Fischer WA, Kanamori H, Sickbert-Bennett EE. Emerging infectious diseases: Focus on infection control issues for novel coronaviruses (Severe Acute Respiratory Syndrome-CoV and Middle East Respiratory Syndrome-CoV), hemorrhagic fever viruses (Lassa and Ebola), and highly pathogenic avian influenza viruses, A(H5N1) and A(H7N9). Am J Infect Control 2016; 44:e91-e100. [PMID: 27131142 PMCID: PMC7132650 DOI: 10.1016/j.ajic.2015.11.018] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 11/11/2015] [Indexed: 01/01/2023]
Abstract
Over the past several decades, we have witnessed the emergence of many new infectious agents, some of which are major public threats. New and emerging infectious diseases which are both transmissible from patient-to-patient and virulent with a high mortality include novel coronaviruses (SARS-CoV, MERS-CV), hemorrhagic fever viruses (Lassa, Ebola), and highly pathogenic avian influenza A viruses, A(H5N1) and A(H7N9). All healthcare facilities need to have policies and plans in place for early identification of patients with a highly communicable diseases which are highly virulent, ability to immediately isolate such patients, and provide proper management (e.g., training and availability of personal protective equipment) to prevent transmission to healthcare personnel, other patients and visitors to the healthcare facility.
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Affiliation(s)
- David J Weber
- Department of Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, NC; Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC.
| | - William A Rutala
- Department of Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, NC; Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC
| | - William A Fischer
- Division of Pulmonary and Critical Care Medicine, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Hajime Kanamori
- Department of Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, NC; Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC
| | - Emily E Sickbert-Bennett
- Department of Hospital Epidemiology, University of North Carolina Health Care, Chapel Hill, NC; Division of Infectious Diseases, University of North Carolina School of Medicine, Chapel Hill, NC
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Abstract
PURPOSE OF REVIEW Attracting global attention, Middle East respiratory syndrome coronavirus (MERS-CoV) continues to cause sporadic cases and a potential risk of healthcare-associated infections. In this review, we highlight what is known about the risk of transmission within healthcare facilities and discuss interventions to halt its transmission within healthcare. RECENT FINDINGS MERS-CoV causes a wide range of infections from asymptomatic infections, mild or moderately symptomatic cases, to fatal disease. Two years after the initial reported case, MERS-CoV has caused limited disease outside the Arabian Peninsula with several cases in Europe, Asia, and the United States. Epidemiologically, these infections are linked to exposures from the region and their diagnosis outside is related to travel. Several reported clusters of disease report multiple transmissions of MERS-CoV within healthcare settings that have been attributed to poor compliance with the basic infection control measures. Factors contributing to the spread and control of MERS-CoV within healthcare settings have not been elucidated so far. Data suggest the overcrowding, late recognition of MERS-CoV cases, and inadequate infection control practices contribute significantly to the transmission. SUMMARY Understanding factors contributing to the spread and the dynamic of MERS-CoV transmission within healthcare settings would further enhance the control of the disease in and outside the healthcare setting.
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Abstract
Middle East respiratory Syndrome Coronavirus (MERS-CoV) has caused at least 1118 reported cases in 24 countries with at least 423 deaths worldwide. All cases are epidemiologically linked to the Arabian Penninsula with most cases reported from the Kingdom of Saudi Arabia. MERS-CoV has three patterns of presentation: sporadic isolated cases, small clusters of intra-familial transmission and large healthcare-associated infections. The disease presentation varies from asymptomatic/mild cases to severe and fatal cases. The source of the virus has focused on bats and dromedary camels but the exact mode of disease transmission continues to be debated. Current data indicate that the virus spreads from human to human through droplet and contact routes, while performing aerosole-generating procedures predispose to airborne transmission. The best diagnostic tests rely on the identification of MERS-CoV by PCR, and lower respiratory tract samples should be favoured for the diagnosis whenever this is possible in order to avoid false negative results. Recently, the World Health Organization added serology to the list of confirmatory tests. Currently, there is no proven therapy, with supportive treatment being the mainstay of treatment.
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Extensive Positive Selection Drives the Evolution of Nonstructural Proteins in Lineage C Betacoronaviruses. J Virol 2016; 90:3627-39. [PMID: 26792741 DOI: 10.1128/jvi.02988-15] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 01/12/2016] [Indexed: 12/14/2022] Open
Abstract
UNLABELLED Middle East respiratory syndrome-related coronavirus (MERS-CoV) spreads to humans via zoonotic transmission from camels. MERS-CoV belongs to lineage C of betacoronaviruses (betaCoVs), which also includes viruses isolated from bats and hedgehogs. A large portion of the betaCoV genome consists of two open reading frames (ORF1a and ORF1b) that are translated into polyproteins. These are cleaved by viral proteases to generate 16 nonstructural proteins (nsp1 to nsp16) which compose the viral replication-transcription complex. We investigated the evolution of ORF1a and ORF1b in lineage C betaCoVs. Results indicated widespread positive selection, acting mostly on ORF1a. The proportion of positively selected sites in ORF1a was much higher than that previously reported for the surface-exposed spike protein. Selected sites were unevenly distributed, with nsp3 representing the preferential target. Several pairs of coevolving sites were also detected, possibly indicating epistatic interactions; most of these were located in nsp3. Adaptive evolution at nsp3 is ongoing in MERS-CoV strains, and two selected sites (G720 and R911) were detected in the protease domain. While position 720 is variable in camel-derived viruses, suggesting that the selective event does not represent a specific adaptation to humans, the R911C substitution was observed only in human-derived MERS-CoV isolates, including the viral strain responsible for the recent South Korean outbreak. It will be extremely important to assess whether these changes affect host range or other viral phenotypes. More generally, data herein indicate that CoV nsp3 represents a major selection target and that nsp3 sequencing should be envisaged in monitoring programs and field surveys. IMPORTANCE Both severe acute respiratory syndrome coronavirus (SARS-CoV) and MERS-CoV originated in bats and spread to humans via an intermediate host. This clearly highlights the potential for coronavirus host shifting and the relevance of understanding the molecular events underlying the adaptation to new host species. We investigated the evolution of ORF1a and ORF1b in lineage C betaCoVs and in 87 sequenced MERS-CoV isolates. Results indicated widespread positive selection, stronger in ORF1a than in ORF1b. Several selected sites were found to be located in functionally relevant protein regions, and some of them corresponded to functional mutations in other coronaviruses. The proportion of selected sites we identified in ORF1a is much higher than that for the surface-exposed spike protein. This observation suggests that adaptive evolution in ORF1a might contribute to host shifts or immune evasion. Data herein also indicate that genetic diversity at nonstructural proteins should be taken into account when antiviral compounds are developed.
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Abstract
The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) poses a potential threat to global public health. Many aspects of the evolution and transmission of MERS-CoV in its animal reservoir remain unclear. A recent study provides new insights into the evolution and transmission of MERS-CoV in dromedary camels.
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Kim JI, Kim YJ, Lemey P, Lee I, Park S, Bae JY, Kim D, Kim H, Jang SI, Yang JS, Kim H, Kim DW, Nam JG, Kim SS, Kim K, Myun Lee J, Song MK, Song D, Chang J, Hong KJ, Bae YS, Song JW, Lee JS, Park MS. The recent ancestry of Middle East respiratory syndrome coronavirus in Korea has been shaped by recombination. Sci Rep 2016; 6:18825. [PMID: 26732651 PMCID: PMC4702133 DOI: 10.1038/srep18825] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 11/23/2015] [Indexed: 01/14/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe cases of human respiratory disease. Since 2012, the victims have mainly come from the Middle East countries or sporadically from some other geographical regions seeded by the travelers who visited the Middle East. Such an introduction through travelling led to the emergence of a MERS-CoV outbreak in Korea in May 2015, which caused more than 140 confirmed human cases in less than a month. Using 70 complete genome sequences of MERS-CoV isolates, including the most recent sequences for the Korean and Chinese isolates, we reconstructed the phylogenetic relationships of the complete genome and the individual protein coding regions. The Korean MERS-CoV strain clustered in the previously established Hafr-Al-Batin-1_2013 clade together with two Saudi Arabian and one Chinese strain sampled in 2015. Although these four strains remained monophyletic in the entire protein-coding region, this clade showed different phylogenetic relationships across the genome, indicating a shared unique recombination pattern that is different from previously reported putative recombination strains. Our findings suggest that the recent ancestor of the Korean and its related MERS-CoV strains is characterized by unique mosaic genome pattern that is different from other putative recombinants.
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Affiliation(s)
- Jin Il Kim
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | | | - Philippe Lemey
- Department of Microbiology and Immunology, Rega Institute, KU Leuven - University of Leuven, Leuven 3000, Belgium
| | - Ilseob Lee
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Sehee Park
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Joon-Yong Bae
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Donghwan Kim
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Hyejin Kim
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Seok-Il Jang
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | | | - Hak Kim
- Division of Respiratory Viruses
| | - Dae-Won Kim
- Division of Biosafety Evaluation and Control
| | | | | | - Kisoon Kim
- Division of Influenza Virus, Center for Infectious Diseases
| | - Jae Myun Lee
- Department of Microbiology and Immunology, Yonsei University College of Medicine, Seoul 120-752, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Man Ki Song
- Laboratory Science Division, International Vaccine Institute, Seoul 151-742, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Daesub Song
- College of Pharmacy, Korea University, Sejong 339-700, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Jun Chang
- Division of Life &Pharmaceutical Sciences, Ewha Womans University, Seoul 120-750, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Kee-Jong Hong
- ATGen, Seongnam 463-400, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Yong-Soo Bae
- Department of Biological Science, Sungkyunkwan University, Suwon 440-746, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
| | - Jin-Won Song
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea
| | - Joo-Shil Lee
- Korea National Institute of Health, Osong 361-951, Republic of Korea
| | - Man-Seong Park
- Department of Microbiology, the Institute for Viral Diseases and Korea Bank for Pathogenic Viruses, College of Medicine, Korea University, Seoul 136-705, Republic of Korea.,The MERS Task Force of the Korean Society of Virology, Seoul 137-701, Republic of Korea
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Mackay IM, Arden KE. MERS coronavirus: diagnostics, epidemiology and transmission. Virol J 2015; 12:222. [PMID: 26695637 PMCID: PMC4687373 DOI: 10.1186/s12985-015-0439-5] [Citation(s) in RCA: 232] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 11/27/2015] [Indexed: 01/04/2023] Open
Abstract
The first known cases of Middle East respiratory syndrome (MERS), associated with infection by a novel coronavirus (CoV), occurred in 2012 in Jordan but were reported retrospectively. The case first to be publicly reported was from Jeddah, in the Kingdom of Saudi Arabia (KSA). Since then, MERS-CoV sequences have been found in a bat and in many dromedary camels (DC). MERS-CoV is enzootic in DC across the Arabian Peninsula and in parts of Africa, causing mild upper respiratory tract illness in its camel reservoir and sporadic, but relatively rare human infections. Precisely how virus transmits to humans remains unknown but close and lengthy exposure appears to be a requirement. The KSA is the focal point of MERS, with the majority of human cases. In humans, MERS is mostly known as a lower respiratory tract (LRT) disease involving fever, cough, breathing difficulties and pneumonia that may progress to acute respiratory distress syndrome, multiorgan failure and death in 20% to 40% of those infected. However, MERS-CoV has also been detected in mild and influenza-like illnesses and in those with no signs or symptoms. Older males most obviously suffer severe disease and MERS patients often have comorbidities. Compared to severe acute respiratory syndrome (SARS), another sometimes- fatal zoonotic coronavirus disease that has since disappeared, MERS progresses more rapidly to respiratory failure and acute kidney injury (it also has an affinity for growth in kidney cells under laboratory conditions), is more frequently reported in patients with underlying disease and is more often fatal. Most human cases of MERS have been linked to lapses in infection prevention and control (IPC) in healthcare settings, with approximately 20% of all virus detections reported among healthcare workers (HCWs) and higher exposures in those with occupations that bring them into close contact with camels. Sero-surveys have found widespread evidence of past infection in adult camels and limited past exposure among humans. Sensitive, validated reverse transcriptase real-time polymerase chain reaction (RT-rtPCR)-based diagnostics have been available almost from the start of the emergence of MERS. While the basic virology of MERS-CoV has advanced over the past three years, understanding of the interplay between camel, environment, and human remains limited.
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Affiliation(s)
- Ian M Mackay
- Department of Health, Public and Environmental Health Virology Laboratory, Forensic and Scientific Services, Archerfield, QLD, Australia.
- The University of Queensland, St Lucia, QLD, Australia.
- Queensland University of Technology, George St, Brisbane, QLD, Australia.
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Reeves T, Samy AM, Peterson AT. MERS-CoV geography and ecology in the Middle East: analyses of reported camel exposures and a preliminary risk map. BMC Res Notes 2015; 8:801. [PMID: 26683322 PMCID: PMC4684610 DOI: 10.1186/s13104-015-1789-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 12/03/2015] [Indexed: 02/02/2023] Open
Abstract
Background Middle Eastern respiratory syndrome coronavirus (MERS-CoV) has spread rapidly across much of the Middle East, but no quantitative mapping of transmission risk has been developed to date. Moreover, details of the transmission cycle of the virus remain unclear, particularly regarding the role of camels as a reservoir host for human infections. Methods We present a first analysis of the environmental circumstances under which MERS-CoV cases have occurred in the Middle East, covering all case occurrences through May 2015, using ecological niche modeling approaches to map transmission risk. We compare the environmental breadth of conditions under which cases have reported camel contacts with that of the broader population of all cases, to assess whether camel-associated cases occur under a more restricted set of environmental circumstances. Results We documented geographic and environmental distributions of MERS-CoV cases across the Middle East, and offer preliminary mapping of transmission risk. We confirm the idea that climatic dimensions of camel-associated cases are more constrained and less variable than the broader suite of case occurrences; hence, camel exposure may be a key limiting element in MERS-CoV transmission. Conclusion This study offers a first detailed geographic and environmental analysis of MERS-CoV distributions across the Middle East. Results indicated that camel-exposed cases occur under a narrower suite of environmental conditions than non-camel-exposed cases, suggesting perhaps a key role for camels in the transmission of the disease, and perhaps a narrower area of risk for ‘primary,’ camel-derived cases of MERS.
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Affiliation(s)
- Tarian Reeves
- Biodiversity Institute, University of Kansas, Lawrence, KS, 66045, USA.
| | - Abdallah M Samy
- Faculty of Science, Ain Shams University, Abbassia, Cairo, 11566, Egypt.
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Poletto C, Colizza V, Boëlle PY. Quantifying spatiotemporal heterogeneity of MERS-CoV transmission in the Middle East region: A combined modelling approach. Epidemics 2015; 15:1-9. [PMID: 27266844 PMCID: PMC7104927 DOI: 10.1016/j.epidem.2015.12.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/28/2015] [Accepted: 12/09/2015] [Indexed: 11/17/2022] Open
Abstract
We modelled MERS epidemic in the Middle East region up to September 2014. We assessed spatiotemporal variation in zoonotic and human transmission. Spring 2014 wave showed a 17-fold and 3-fold increase in the above transmissions. Zoonotic transmission has a larger spatial heterogeneity than human transmission. Human transmission is more frequent than expected (75% of cases vs. 34%).
MERS coronavirus cases notified in the Middle East region since the identification of the virus in 2012 have displayed variations in time and across geography. Through a combined modelling approach, we estimate the rates of generation of cases along the zoonotic and human-to-human transmission routes and assess their spatiotemporal heterogeneity. We consider all cases notified to WHO from March 2012 to mid-September 2014. We use a stochastic modelling of the time series of case incidence in the Middle East region to estimate time- and space-dependent zoonotic and human-to-human transmission parameters. The model also accounts for possible lack of identification of secondary transmissions among notified cases. This approach is combined with the analysis of imported cases out of the region to assess the rate of underreporting of cases. Out of a total of 32 possible models, based on different parameterisation and scenario considered, the best-fit model is characterised by a large heterogeneity in time and across space for both zoonotic and human-to-human transmission. The variation in time that occurred during Spring 2014 led to a 17-fold and 3-fold increase in the two transmissions, respectively, bringing the reproductive rate to values above 1 during that period for all regions under study. The model suggests that 75% of MERS-CoV cases are secondary cases (human-to-human transmission), which is substantially higher than the 34% of reported cases with an epidemiological link to another case. Overall, estimated reporting rate is 0.26. Our findings show a higher level of spatial heterogeneity in zoonotic transmission compared to human-to-human, highlighting the strong environmental component of the epidemic. Since sporadic introductions are predicted to be a small proportion of notified cases and are responsible for triggering secondary transmissions, a more comprehensive understanding of zoonotic source and path of transmission could be critical to limit the epidemic spread.
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Affiliation(s)
- Chiara Poletto
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75012, 27 rue Chaligny, Paris 75012, France.
| | - Vittoria Colizza
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75012, 27 rue Chaligny, Paris 75012, France; Institute for Scientific Interchange Foundation, via Alassio 11/c, Torino 10126, Italy
| | - Pierre-Yves Boëlle
- Sorbonne Universités, UPMC Univ Paris 06, INSERM, Institut Pierre Louis d'épidémiologie et de Santé Publique (IPLESP UMRS 1136), F75012, 27 rue Chaligny, Paris 75012, France
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Zhang L, Hao M, Zhang K, Zhang R, Lin G, Jia T, Zhang D, Chang L, Xie J, Li J. External quality assessment for the molecular detection of MERS-CoV in China. J Clin Virol 2015; 75:5-9. [PMID: 26702992 PMCID: PMC7106428 DOI: 10.1016/j.jcv.2015.12.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/25/2015] [Accepted: 12/07/2015] [Indexed: 12/17/2022]
Abstract
BACKGROUND In May 2015, an imported case of Middle East respiratory syndrome coronavirus (MERS-CoV) infection occurred in China, so rapid and reliable diagnosis of suspected cases was necessary. OBJECTIVES An external quality assessment (EQA) program for the molecular detection of MERS-CoV was organized by the National Center for Clinical Laboratories (NCCL). STUDY DESIGN MS2 virus-like particles (VLPs) encapsulating specific RNA sequences of MERS-CoV were prepared as positive specimens. The assessment panel, which comprised of three negative and seven positive samples with different concentrations of VLPs, was distributed to 56 laboratories from 16 provinces, municipalities, or autonomous regions for molecular detection. RESULTS Among the received data sets, three employed an in-house-developed real-time reverse-transcription polymerase chain reaction (rRT-PCR) assay and the others applied various commercial rRT-PCR kits. Overall, the majority of laboratories (46/56, 82.1%) could achieve 100% accuracy for MERS-CoV detection, but three laboratories (5.4%) still had room for improvement. Consequently, all negative samples were identified correctly, reaching 100% specificity. The false-negative rate was 3.1%, and most of the false-negative results were obtained from samples with relatively low concentration, indicating an urgent need to improve detection in weak-positive specimens. CONCLUSIONS The majority of participants possessed reliable diagnostic capacity for the detection of MERS-CoV. Moreover, EQA is indispensable because it can help enhance the diagnostic capability for the surveillance of MERS-CoV infections and allow comparison of the results among different laboratories.
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Affiliation(s)
- Lei Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China; Peking University Fifth School of Clinical Medicine, Beijing, PR China
| | - Mingju Hao
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China
| | - Rui Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China
| | - Guigao Lin
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China
| | - Tingting Jia
- Department of Clinical Laboratory, Beijing Chaoyang Hospital Affiliated to the Capital University of Medical Sciences, Beijing, PR China
| | - Dong Zhang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Le Chang
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jiehong Xie
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China
| | - Jinming Li
- National Center for Clinical Laboratories, Beijing Hospital, Beijing, PR China; Peking University Fifth School of Clinical Medicine, Beijing, PR China.
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Johnson PTJ, de Roode JC, Fenton A. Why infectious disease research needs community ecology. Science 2015; 349:1259504. [PMID: 26339035 DOI: 10.1126/science.1259504] [Citation(s) in RCA: 256] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Infectious diseases often emerge from interactions among multiple species and across nested levels of biological organization. Threats as diverse as Ebola virus, human malaria, and bat white-nose syndrome illustrate the need for a mechanistic understanding of the ecological interactions underlying emerging infections. We describe how recent advances in community ecology can be adopted to address contemporary challenges in disease research. These analytical tools can identify the factors governing complex assemblages of multiple hosts, parasites, and vectors, and reveal how processes link across scales from individual hosts to regions. They can also determine the drivers of heterogeneities among individuals, species, and regions to aid targeting of control strategies. We provide examples where these principles have enhanced disease management and illustrate how they can be further extended.
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Affiliation(s)
- Pieter T J Johnson
- Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA.
| | | | - Andy Fenton
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
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The heptad repeat region is a major selection target in MERS-CoV and related coronaviruses. Sci Rep 2015; 5:14480. [PMID: 26404138 PMCID: PMC4585914 DOI: 10.1038/srep14480] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2015] [Accepted: 09/01/2015] [Indexed: 01/08/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) originated in bats and spread to humans via zoonotic transmission from camels. We analyzed the evolution of the spike (S) gene in betacoronaviruses (betaCoVs) isolated from different mammals, in bat coronavirus populations, as well as in MERS-CoV strains from the current outbreak. Results indicated several positively selected sites located in the region comprising the two heptad repeats (HR1 and HR2) and their linker. Two sites (R652 and V1060) were positively selected in the betaCoVs phylogeny and correspond to mutations associated with expanded host range in other coronaviruses. During the most recent evolution of MERS-CoV, adaptive mutations in the HR1 (Q/R/H1020) arose in camels or in a previous host and spread to humans. We determined that different residues at position 1020 establish distinct inter- and intra-helical interactions and affect the stability of the six-helix bundle formed by the HRs. A similar effect on stability was observed for a nearby mutation (T1015N) that increases MERS-CoV infection efficiency in vitro. Data herein indicate that the heptad repeat region was a major target of adaptive evolution in MERS-CoV-related viruses; these results are relevant for the design of fusion inhibitor peptides with antiviral function.
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Durai P, Batool M, Shah M, Choi S. Middle East respiratory syndrome coronavirus: transmission, virology and therapeutic targeting to aid in outbreak control. Exp Mol Med 2015; 47:e181. [PMID: 26315600 PMCID: PMC4558490 DOI: 10.1038/emm.2015.76] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 08/05/2015] [Indexed: 12/17/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes high fever, cough, acute respiratory tract infection and multiorgan dysfunction that may eventually lead to the death of the infected individuals. MERS-CoV is thought to be transmitted to humans through dromedary camels. The occurrence of the virus was first reported in the Middle East and it subsequently spread to several parts of the world. Since 2012, about 1368 infections, including ~487 deaths, have been reported worldwide. Notably, the recent human-to-human 'superspreading' of MERS-CoV in hospitals in South Korea has raised a major global health concern. The fatality rate in MERS-CoV infection is four times higher compared with that of the closely related severe acute respiratory syndrome coronavirus infection. Currently, no drug has been clinically approved to control MERS-CoV infection. In this study, we highlight the potential drug targets that can be used to develop anti-MERS-CoV therapeutics.
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Affiliation(s)
| | - Maria Batool
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology, Ajou University, Suwon, Korea
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Lu G, Wang Q, Gao GF. Bat-to-human: spike features determining 'host jump' of coronaviruses SARS-CoV, MERS-CoV, and beyond. Trends Microbiol 2015. [PMID: 26206723 PMCID: PMC7125587 DOI: 10.1016/j.tim.2015.06.003] [Citation(s) in RCA: 394] [Impact Index Per Article: 43.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Bats are natural reservoirs of many coronaviruses that can infect humans. Mechanisms of cross-species transmission of coronaviruses are important scientific questions. The coronaviral spike protein is an important viral determinant of cross-species transmission. Receptor-binding characteristics and cleavage priming of the spike protein are summarized.
Both severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) are zoonotic pathogens that crossed the species barriers to infect humans. The mechanism of viral interspecies transmission is an important scientific question to be addressed. These coronaviruses contain a surface-located spike (S) protein that initiates infection by mediating receptor-recognition and membrane fusion and is therefore a key factor in host specificity. In addition, the S protein needs to be cleaved by host proteases before executing fusion, making these proteases a second determinant of coronavirus interspecies infection. Here, we summarize the progress made in the past decade in understanding the cross-species transmission of SARS-CoV and MERS-CoV by focusing on the features of the S protein, its receptor-binding characteristics, and the cleavage process involved in priming.
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Affiliation(s)
- Guangwen Lu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan, China.
| | - Qihui Wang
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; CAS Key Laboratory of Microbial Physiological and Metabolic Engineering, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - George F Gao
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Office of Director-General, Chinese Center for Disease Control and Prevention (China CDC), Beijing 102206, China.
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Memish ZA, Al-Tawfiq JA, Alhakeem RF, Assiri A, Alharby KD, Almahallawi MS, Alkhallawi M. Middle East respiratory syndrome coronavirus (MERS-CoV): A cluster analysis with implications for global management of suspected cases. Travel Med Infect Dis 2015; 13:311-4. [PMID: 26211569 PMCID: PMC7110629 DOI: 10.1016/j.tmaid.2015.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Revised: 06/27/2015] [Accepted: 06/29/2015] [Indexed: 01/02/2023]
Abstract
Since the initial description of the Middle East respiratory syndrome (MERS) in September 2012, a total of 1038 cases of MERS-CoV including 460 deaths have been reported from Saudi Arabia. From August 24, 2013 to September 3, 2013, a total of 397 patients and contacts were tested for MERS-CoV. Of those tested, there were 18 (4.5%) MERS-CoV cases reported in Al-Madinah al-Munawwarah with one large cluster. In this report, we describe the outcome, epidemiology and clinical characteristics of this cluster of which 4 cases involved healthcare workers. Fourteen cases appeared to be linked to one cluster involving healthcare workers (HCWs), family and patient contacts. Of the 18 cases, five (including 2 HCWs) were community acquired, two were household contacts, and 11 were healthcare associated (including 4 HCWs). All except 4 cases were symptomatic and the case fatality rate was 39% (7 of 18). The outbreak resulted in human to human transmission of an estimated 6 cases. Contact screening showed positive test in 1 of 56 (1.8%) household contacts, and 3 of 250 (1.2%) HCWs.
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Affiliation(s)
- Ziad A Memish
- Ministry of Health, Riyadh, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Jaffar A Al-Tawfiq
- Johns Hopkins Aramco Healthcare, Dhahran, Saudi Arabia; Indiana University School of Medicine, Indianapolis, IN, USA.
| | | | | | - Khalid D Alharby
- Regional Health Directorate, Ministry of Health, Madinah, Saudi Arabia
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Banik GR, Khandaker G, Rashid H. Middle East respiratory syndrome coronavirus "MERS-CoV": current knowledge gaps. Paediatr Respir Rev 2015; 16:197-202. [PMID: 26002405 PMCID: PMC7106011 DOI: 10.1016/j.prrv.2015.04.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 04/09/2015] [Indexed: 12/20/2022]
Abstract
The Middle East respiratory syndrome coronavirus (MERS-CoV) that causes a severe lower respiratory tract infection in humans is now considered a pandemic threat to the Gulf region. Since its discovery in 2012, MERS-CoV has reached 23 countries affecting about 1100 people, including a dozen children, and claiming over 400 lives. Compared to SARS (severe acute respiratory syndrome), MERS-CoV appears to kill more people (40% versus 10%), more quickly, and is especially more severe in those with pre-existing medical conditions. Most MERS-CoV cases (>85%) reported thus far have a history of residence in, or travel to the Middle East. The current epidemiology is characterised by slow and sustained transmission with occasional sparks. The dromedary camel is the intermediate host of MERS-CoV, but the transmission cycle is not fully understood. In this current review, we have briefly summarised the latest information on the epidemiology, clinical features, diagnosis, treatment and prevention of MERS-CoV especially highlighting the knowledge gaps in its transmission dynamics, diagnosis and preventive strategy.
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Affiliation(s)
- G R Banik
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, The Children's Hospital at Westmead, Westmead, NSW, Australia; University of Technology Sydney, School of Medical and Molecular Biosciences, Broadway, Sydney, NSW, Australia.
| | - G Khandaker
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, The Children's Hospital at Westmead, Westmead, NSW, Australia; Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia; Centre for Perinatal Infection Research, The Children's Hospital at Westmead and The University of Sydney, Sydney, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, the University of Sydney, Sydney, NSW, Australia
| | - H Rashid
- National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases, The Children's Hospital at Westmead, Westmead, NSW, Australia; Discipline of Paediatrics and Child Health, Sydney Medical School, The University of Sydney, Sydney, NSW, Australia; Marie Bashir Institute for Infectious Diseases and Biosecurity, the University of Sydney, Sydney, NSW, Australia
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Protective Efficacy of Recombinant Modified Vaccinia Virus Ankara Delivering Middle East Respiratory Syndrome Coronavirus Spike Glycoprotein. J Virol 2015; 89:8651-6. [PMID: 26018172 DOI: 10.1128/jvi.00614-15] [Citation(s) in RCA: 124] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/23/2015] [Indexed: 12/12/2022] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes severe respiratory disease in humans. We tested a recombinant modified vaccinia virus Ankara (MVA) vaccine expressing full-length MERS-CoV spike (S) glycoprotein by immunizing BALB/c mice with either intramuscular or subcutaneous regimens. In all cases, MVA-MERS-S induced MERS-CoV-specific CD8(+) T cells and virus-neutralizing antibodies. Vaccinated mice were protected against MERS-CoV challenge infection after transduction with the human dipeptidyl peptidase 4 receptor. This MERS-CoV infection model demonstrates the safety and efficacy of the candidate vaccine.
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Parry-Ford F, Boddington N, Pebody R, Phin N. Public health response to two incidents of confirmed MERS-CoV cases travelling on flights through London Heathrow Airport in 2014 – lessons learnt. ACTA ACUST UNITED AC 2015; 20. [PMID: 25990234 DOI: 10.2807/1560-7917.es2015.20.18.21114] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In May 2014, Public Health England was alerted to two separate laboratory-confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection who transited through London Heathrow Airport while symptomatic on flights from Saudi Arabia to the United States of America. We present the rationale for the public health response to both incidents, and report results of contact tracing. Following a risk assessment, passengers seated two seats around the cases were prioritised for contact tracing and a proactive media approach was used to alert all passengers on the planes of their possible exposure in both incidents. In total, 64 United Kingdom (UK) residents were successfully contacted, 14 of whom were sat in the priority area two seats all around the case(s). Five passengers reported respiratory symptoms within 14 days of the flight, but all tested were negative for MERS-CoV. Details of non-UK residents were passed on to relevant World Health Organization International Health Regulation focal points for follow-up, and no further cases were reported back. Different approaches were used to manage contact tracing for each flight due to variations in the quality and timeliness of the passenger contact information provided by the airlines involved. No evidence of symptomatic onward transmission was found.
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Affiliation(s)
- F Parry-Ford
- Centre for Infectious Disease Surveillance and Control, Public Health England, London, United Kingdom
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