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So RTY, Chu DKW, Hui KPY, Mok CKP, Shum MHH, Sanyal S, Nicholls JM, Ho JCW, Cheung MC, Ng KC, Yeung HW, Chan MCW, Poon LLM, Zhao J, Lam TTY, Peiris M. Amino acid substitution L232F in non-structural protein 6 identified as a possible human-adaptive mutation in clade B MERS coronaviruses. J Virol 2023; 97:e0136923. [PMID: 38038429 PMCID: PMC10734512 DOI: 10.1128/jvi.01369-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 11/09/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE Viral host adaptation plays an important role in inter-species transmission of coronaviruses and influenza viruses. Multiple human-adaptive mutations have been identified in influenza viruses but not so far in MERS-CoV that circulates widely in dromedary camels in the Arabian Peninsula leading to zoonotic transmission. Here, we analyzed clade B MERS-CoV sequences and identified an amino acid substitution L232F in nsp6 that repeatedly occurs in human MERS-CoV. Using a loss-of-function reverse genetics approach, we found the nsp6 L232F conferred increased viral replication competence in vitro, in cultures of the upper human respiratory tract ex vivo, and in lungs of mice infected in vivo. Our results showed that nsp6 L232F may be an adaptive mutation associated with zoonotic transmission of MERS-CoV. This study highlighted the capacity of MERS-CoV to adapt to transmission to humans and also the need for continued surveillance of MERS-CoV in camels.
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Affiliation(s)
- Ray T. Y. So
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
| | - Daniel K. W. Chu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- UK Health Security Agency, London, United Kingdom
| | - Kenrie P. Y. Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Chris K. P. Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Marcus H. H. Shum
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - John M. Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - John C. W. Ho
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Man-chun Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Ka-chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Hin-Wo Yeung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Michael C. W. Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Leo L. M. Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of 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, People's Republic of China
| | - Tommy T. Y. Lam
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People's Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People's Republic of China
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Soto R, Paul L, Porucznik CA, Xie H, Stinnett RC, Briggs B, Biggerstaff M, Stanford J, Schlaberg R. Effectiveness of Self-Collected, Ambient Temperature-Preserved Nasal Swabs Compared to Samples Collected by Trained Staff for Genotyping of Respiratory Viruses by Shotgun RNA Sequencing: Comparative Study. JMIR Form Res 2023; 7:e32848. [PMID: 37999952 DOI: 10.2196/32848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 02/16/2023] [Accepted: 08/09/2023] [Indexed: 11/25/2023] Open
Abstract
BACKGROUND The SARS-CoV-2 pandemic has underscored the need for field specimen collection and transport to diagnostic and public health laboratories. Self-collected nasal swabs transported without dependency on a cold chain have the potential to remove critical barriers to testing, expand testing capacity, and reduce opportunities for exposure of health professionals in the context of a pandemic. OBJECTIVE We compared nasal swab collection by study participants from themselves and their children at home to collection by trained research staff. METHODS Each adult participant collected 1 nasal swab, sampling both nares with the single swab, after which they collected 1 nasal swab from 1 child. After all the participant samples were collected for the household, the research staff member collected a separate single duplicate sample from each individual. Immediately after the sample collection, the adult participants completed a questionnaire about the acceptability of the sampling procedures. Swabs were placed in temperature-stable preservative and respiratory viruses were detected by shotgun RNA sequencing, enabling viral genome analysis. RESULTS In total, 21 households participated in the study, each with 1 adult and 1 child, yielding 42 individuals with paired samples. Study participants reported that self-collection was acceptable. Agreement between identified respiratory viruses in both swabs by RNA sequencing demonstrated that adequate collection technique was achieved by brief instructions. CONCLUSIONS Our results support the feasibility of a scalable and convenient means for the identification of respiratory viruses and implementation in pandemic preparedness for novel respiratory pathogens.
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Affiliation(s)
- Raymond Soto
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Litty Paul
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Christina A Porucznik
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Heng Xie
- IDbyDNA, Salt Lake City, UT, United States
| | | | | | - Matthew Biggerstaff
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Joseph Stanford
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
| | - Robert Schlaberg
- Department of Family and Preventive Medicine, University of Utah, Salt Lake City, UT, United States
- IDbyDNA, Salt Lake City, UT, United States
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So RTY, Chu DKW, Hui KPY, Mok CKP, Sanyal S, Nicholls JM, Ho JCW, Cheung MC, Ng KC, Yeung HW, Chan MCW, Poon LLM, Zhao J, Peiris M. Mutation nsp6 L232F associated with MERS-CoV zoonotic transmission confers higher viral replication in human respiratory tract cultures ex-vivo. bioRxiv 2023:2023.03.27.534490. [PMID: 37034576 PMCID: PMC10081289 DOI: 10.1101/2023.03.27.534490] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) causes zoonotic disease. Dromedary camels are the source of zoonotic infection. We identified a mutation of amino acid leucine to phenylalanine in the codon 232 position of the non-structural protein 6 (nsp6) (nsp6 L232F) that is repeatedly associated with zoonotic transmission. We generated a pair of isogenic recombinant MERS-CoV with nsp6 232L and 232F residues, respectively, and showed that the nsp6 L232F mutation confers higher replication competence in ex-vivo culture of human nasal and bronchial tissues and in lungs of mice experimentally infected in-vivo. Mechanistically, the nsp6 L232F mutation appeared to modulate autophagy and was associated with higher exocytic virus egress, while innate immune responses and zippering activity of the endoplasmic reticulum remained unaffected. Our study suggests that MERS-CoV nsp6 may contribute to viral adaptation to humans. This highlights the importance of continued surveillance of MERS-CoV in both camels and humans.
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Affiliation(s)
- Ray TY So
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
| | - Daniel KW Chu
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- UK Health Security Agency, London, United Kingdom
| | - Kenrie PY Hui
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Chris KP Mok
- The Jockey Club School of Public Health and Primary Care, The Chinese University of Hong Kong, Hong Kong SAR, PR China
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Sumana Sanyal
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - John M Nicholls
- Department of Pathology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - John C. W. Ho
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Man-chun Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Ka-chun Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Hin-Wo Yeung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Michael CW Chan
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
| | - Leo LM Poon
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of 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, People’s Republic of China
| | - Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region, People’s Republic of China
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Zhao Y, Liang R, Cheng J, Zhao J, Xue J, Zhang G. Attenuated Viral Replication of Avian Infectious Bronchitis Virus with a Novel 82-Nucleotide Deletion in the 5a Gene Indicates a Critical Role for 5a in Virus-Host Interactions. Microbiol Spectr 2022;:e0140522. [PMID: 35766501 DOI: 10.1128/spectrum.01405-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We previously found that a deletion in γ-coronavirus Infectious bronchitis virus (IBV) accessory gene 5a is critical for decreased viral pathogenicity in chickens. Here, we systematically analyzed IBV virus infection: invasion, genome replication, subgenomic mRNA (sgmRNA) synthesis, protein synthesis, and virion release. The ability of the mutant IBV strain rYN-Δ5a to invade susceptible cells was not significantly different from that of parental rYN. However, compared with rYN, the level of sgmRNA synthesis and genome replication after cell entry by rYN-Δ5a was significantly lower in the early stage, resulting in a significantly lower level of nucleoprotein (N) synthesis and a consequent significantly lower number of offspring viruses released into the supernatant. The detected 5a protein was diffusely distributed in the cytoplasm and perinuclear area. We identified 16 differentially expressed host proteins, 8 of which were found to be host nuclear and cytoplasmic transport-related proteins. Coimmunoprecipitation revealed an interaction between hemagglutinin (HA)-tagged TNPO1, TNPO3, XPO1, XPOT, RanBP1, and EIF2B4 proteins and Flag-tagged 5a protein, and laser confocal microscopy confirmed 5a protein colocalization with these proteins, indicating that 5a protein can cause changes in the host protein localization. These host proteins promote the nuclear localization of N proteins, so we believe that 5a protein can hijack host nucleoplasmic transport-related proteins to help N enter the nucleus. This may involve regulating the cell cycle to promote the optimal intracellular conditions for virus assembly or by participating in the regulation of nucleolar function as a strategy to optimize virus replication. IMPORTANCE Coronaviruses (CoVs) have a huge impact on humans and animals. It is important for the prevention and control of the viruses to assess the molecular mechanisms related to virulence attenuation. Here, we systematically analyzed a single cycle of virus infection by γ-CoV IBV lacking accessory protein 5a. We observed that a 5a deletion in the IBV genome affected virus replication and sgmRNA synthesis early in the virus life cycle, leading to decreases in protein synthesis, offspring virus assembly, and virion release in chicken embryonic kidney cells. IBV 5a protein was found to interact with multiple host nuclear and cytoplasmic transport- and translation-related proteins, which can also interact with IBV N and relocate it into the cell nucleus. These findings provide a comprehensive view regarding the importance of IBV accessory protein 5a and an important theoretical basis for studying the interaction between coronavirus and host cell proteins.
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Hoteit R, Yassine HM. Biological Properties of SARS-CoV-2 Variants: Epidemiological Impact and Clinical Consequences. Vaccines (Basel) 2022; 10:919. [PMID: 35746526 PMCID: PMC9230982 DOI: 10.3390/vaccines10060919] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 05/18/2022] [Accepted: 05/21/2022] [Indexed: 02/06/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a virus that belongs to the coronavirus family and is the cause of coronavirus disease 2019 (COVID-19). As of May 2022, it had caused more than 500 million infections and more than 6 million deaths worldwide. Several vaccines have been produced and tested over the last two years. The SARS-CoV-2 virus, on the other hand, has mutated over time, resulting in genetic variation in the population of circulating variants during the COVID-19 pandemic. It has also shown immune-evading characteristics, suggesting that vaccinations against these variants could be potentially ineffective. The purpose of this review article is to investigate the key variants of concern (VOCs) and mutations of the virus driving the current pandemic, as well as to explore the transmission rates of SARS-CoV-2 VOCs in relation to epidemiological factors and to compare the virus's transmission rate to that of prior coronaviruses. We examined and provided key information on SARS-CoV-2 VOCs in this study, including their transmissibility, infectivity rate, disease severity, affinity for angiotensin-converting enzyme 2 (ACE2) receptors, viral load, reproduction number, vaccination effectiveness, and vaccine breakthrough.
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Affiliation(s)
- Reem Hoteit
- Clinical Research Institute, Faculty of Medicine, American University of Beirut, Beirut 110236, Lebanon;
| | - Hadi M. Yassine
- Biomedical Research Center and College of Health Sciences-QU Health, Qatar University, Doha 2713, Qatar
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Duault H, Durand B, Canini L. Methods Combining Genomic and Epidemiological Data in the Reconstruction of Transmission Trees: A Systematic Review. Pathogens 2022; 11:252. [PMID: 35215195 PMCID: PMC8875843 DOI: 10.3390/pathogens11020252] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 02/08/2022] [Accepted: 02/11/2022] [Indexed: 11/17/2022] Open
Abstract
In order to better understand transmission dynamics and appropriately target control and preventive measures, studies have aimed to identify who-infected-whom in actual outbreaks. Numerous reconstruction methods exist, each with their own assumptions, types of data, and inference strategy. Thus, selecting a method can be difficult. Following PRISMA guidelines, we systematically reviewed the literature for methods combing epidemiological and genomic data in transmission tree reconstruction. We identified 22 methods from the 41 selected articles. We defined three families according to how genomic data was handled: a non-phylogenetic family, a sequential phylogenetic family, and a simultaneous phylogenetic family. We discussed methods according to the data needed as well as the underlying sequence mutation, within-host evolution, transmission, and case observation. In the non-phylogenetic family consisting of eight methods, pairwise genetic distances were estimated. In the phylogenetic families, transmission trees were inferred from phylogenetic trees either simultaneously (nine methods) or sequentially (five methods). While a majority of methods (17/22) modeled the transmission process, few (8/22) took into account imperfect case detection. Within-host evolution was generally (7/8) modeled as a coalescent process. These practical and theoretical considerations were highlighted in order to help select the appropriate method for an outbreak.
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Jonsdottir HR, Bielecki M, Siegrist D, Buehrer TW, Züst R, Deuel JW. Titers of Neutralizing Antibodies against SARS-CoV-2 Are Independent of Symptoms of Non-Severe COVID-19 in Young Adults. Viruses 2021; 13:v13020284. [PMID: 33673067 PMCID: PMC7918933 DOI: 10.3390/v13020284] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/08/2021] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Neutralizing antibodies are an important part of the humoral immune response to SARS-CoV-2. It is currently unclear to what extent such antibodies are produced after non-severe disease or asymptomatic infection. We studied a cluster of SARS-CoV-2 infections among a homogeneous population of 332 predominantly male Swiss soldiers and determined the neutralizing antibody response with a serum neutralization assay using a recombinant SARS-CoV-2-GFP. All patients with non-severe COVID-19 showed a swift humoral response within two weeks after the onset of symptoms, which remained stable for the duration of the study. One month after the outbreak, titers in COVID-19 convalescents did not differ from the titers of asymptomatically infected individuals. Furthermore, symptoms of COVID-19 did not correlate with neutralizing antibody titers. Therefore, we conclude that asymptomatic infection can induce the same humoral immunity as non-severe COVID-19 in young adults.
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Affiliation(s)
| | - Michel Bielecki
- Swiss Armed Forces, Medical Services, Worblentalstrasse, 3063 Ittigen, Switzerland; (M.B.); (T.W.B.)
- Epidemiology, Biostatistics and Prevention Institute, Travel Clinic, Hirschengraben, University of Zurich, 8006 Zürich, Switzerland
| | - Denise Siegrist
- SPIEZ Laboratory, Austrasse, 3700 Spiez, Switzerland; (H.R.J.); (D.S.)
| | - Thomas W. Buehrer
- Swiss Armed Forces, Medical Services, Worblentalstrasse, 3063 Ittigen, Switzerland; (M.B.); (T.W.B.)
| | - Roland Züst
- SPIEZ Laboratory, Austrasse, 3700 Spiez, Switzerland; (H.R.J.); (D.S.)
- Correspondence: (R.Z.); (J.W.D.)
| | - Jeremy W. Deuel
- Swiss Armed Forces, Medical Services, Worblentalstrasse, 3063 Ittigen, Switzerland; (M.B.); (T.W.B.)
- Jeffrey Cheah Biomedical Centre, Department of Haematology and MRC—Wellcome Stem Cell Institute, Puddicombe Way, University of Cambridge, Cambridge CB2 AW, UK
- Correspondence: (R.Z.); (J.W.D.)
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Kim M, Cho H, Lee SH, Park WJ, Kim JM, Moon JS, Kim GW, Lee W, Jung HG, Yang JS, Choi JH, Lee JY, Kim SS, Oh JW. An infectious cDNA clone of a growth attenuated Korean isolate of MERS coronavirus KNIH002 in clade B. Emerg Microbes Infect 2021; 9:2714-2726. [PMID: 33295839 PMCID: PMC7782039 DOI: 10.1080/22221751.2020.1861914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The MERS-CoV isolated during the 2015 nosocomial outbreak in Korea showed distinctive differences in mortality and transmission patterns compared to the prototype MERS-CoV EMC strain belonging to clade A. We established a BAC-based reverse genetics system for a Korean isolate of MERS-CoV KNIH002 in the clade B phylogenetically far from the EMC strain, and generated a recombinant MERS-CoV expressing red fluorescent protein. The virus rescued from the infectious clone and KNIH002 strain displayed growth attenuation compared to the EMC strain. Consecutive passages of the rescued virus rapidly generated various ORF5 variants, highlighting its genetic instability and calling for caution in the use of repeatedly passaged virus in pathogenesis studies and for evaluation of control measures against MERS-CoV. The infectious clone for the KNIH002 in contemporary epidemic clade B would be useful for better understanding of a functional link between molecular evolution and pathophysiology of MERS-CoV by comparative studies with EMC strain.
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Affiliation(s)
- Minwoo Kim
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Hee Cho
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Seung-Hoon Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Woo-Jung Park
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Jeong-Min Kim
- Division of Viral Diseases, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Jae-Su Moon
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Geon-Woo Kim
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Wooseong Lee
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Hae-Gwang Jung
- Department of Biotechnology, Yonsei University, Seoul, Korea
| | - Jeong-Sun Yang
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Jang-Hoon Choi
- Division of Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Joo-Yeon Lee
- Division of Emerging Infectious Disease and Vector Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Kore
| | - Sung Soon Kim
- Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, Republic of Korea
| | - Jong-Won Oh
- Department of Biotechnology, Yonsei University, Seoul, Korea
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AL-Eitan LN, Tarkhan AH, Alghamdi MA, Marston DA, Wu G, McElhinney LM, Brown IH, Fooks AR. Bat-Borne Coronaviruses in Jordan and Saudi Arabia: A Threat to Public Health? Viruses 2020; 12:E1413. [PMID: 33316899 PMCID: PMC7764733 DOI: 10.3390/v12121413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/22/2022] Open
Abstract
Emerging infectious diseases are of great concern to public health, as highlighted by the ongoing coronavirus disease 2019 (COVID-19) pandemic. Such diseases are of particular danger during mass gathering and mass influx events, as large crowds of people in close proximity to each other creates optimal opportunities for disease transmission. The Hashemite Kingdom of Jordan and the Kingdom of Saudi Arabia are two countries that have witnessed mass gatherings due to the arrival of Syrian refugees and the annual Hajj season. The mass migration of people not only brings exotic diseases to these regions but also brings new diseases back to their own countries, e.g., the outbreak of MERS in South Korea. Many emerging pathogens originate in bats, and more than 30 bat species have been identified in these two countries. Some of those bat species are known to carry viruses that cause deadly diseases in other parts of the world, such as the rabies virus and coronaviruses. However, little is known about bats and the pathogens they carry in Jordan and Saudi Arabia. Here, the importance of enhanced surveillance of bat-borne infections in Jordan and Saudi Arabia is emphasized, promoting the awareness of bat-borne diseases among the general public and building up infrastructure and capability to fill the gaps in public health preparedness to prevent future pandemics.
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Affiliation(s)
- Laith N. AL-Eitan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Amneh H. Tarkhan
- Department of Biotechnology and Genetic Engineering, Jordan University of Science and Technology, Irbid 22110, Jordan;
| | - Mansour A. Alghamdi
- Department of Anatomy, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia;
- Genomics and Personalized Medicine Unit, College of Medicine, King Khalid University, Abha 61421, Saudi Arabia
| | - Denise A. Marston
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Guanghui Wu
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Lorraine M. McElhinney
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Ian H. Brown
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
| | - Anthony R. Fooks
- Department of Virology, Animal and Plant Health Agency (APHA, Weybridge), Surrey KT15 3NB, UK; (D.A.M.); (G.W.); (L.M.M.); (I.H.B.); (A.R.F.)
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Abstract
Importance Crowded indoor environments, such as households, are high-risk settings for the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Objectives To examine evidence for household transmission of SARS-CoV-2, disaggregated by several covariates, and to compare it with other coronaviruses. Data Source PubMed, searched through October 19, 2020. Search terms included SARS-CoV-2 or COVID-19 with secondary attack rate, household, close contacts, contact transmission, contact attack rate, or family transmission. Study Selection All articles with original data for estimating household secondary attack rate were included. Case reports focusing on individual households and studies of close contacts that did not report secondary attack rates for household members were excluded. Data Extraction and Synthesis Meta-analyses were done using a restricted maximum-likelihood estimator model to yield a point estimate and 95% CI for secondary attack rate for each subgroup analyzed, with a random effect for each study. To make comparisons across exposure types, study was treated as a random effect, and exposure type was a fixed moderator. The Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) reporting guideline was followed. Main Outcomes and Measures Secondary attack rate for SARS-CoV-2, disaggregated by covariates (ie, household or family contact, index case symptom status, adult or child contacts, contact sex, relationship to index case, adult or child index cases, index case sex, number of contacts in household) and for other coronaviruses. Results A total of 54 relevant studies with 77 758 participants reporting household secondary transmission were identified. Estimated household secondary attack rate was 16.6% (95% CI, 14.0%-19.3%), higher than secondary attack rates for SARS-CoV (7.5%; 95% CI, 4.8%-10.7%) and MERS-CoV (4.7%; 95% CI, 0.9%-10.7%). Household secondary attack rates were increased from symptomatic index cases (18.0%; 95% CI, 14.2%-22.1%) than from asymptomatic index cases (0.7%; 95% CI, 0%-4.9%), to adult contacts (28.3%; 95% CI, 20.2%-37.1%) than to child contacts (16.8%; 95% CI, 12.3%-21.7%), to spouses (37.8%; 95% CI, 25.8%-50.5%) than to other family contacts (17.8%; 95% CI, 11.7%-24.8%), and in households with 1 contact (41.5%; 95% CI, 31.7%-51.7%) than in households with 3 or more contacts (22.8%; 95% CI, 13.6%-33.5%). Conclusions and Relevance The findings of this study suggest that given that individuals with suspected or confirmed infections are being referred to isolate at home, households will continue to be a significant venue for transmission of SARS-CoV-2.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, Washington
- Department of Biostatistics, University of Washington, Seattle
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville
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12
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Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Household transmission of SARS-CoV-2: a systematic review and meta-analysis of secondary attack rate. medRxiv 2020:2020.07.29.20164590. [PMID: 32766596 PMCID: PMC7402051 DOI: 10.1101/2020.07.29.20164590] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is spread by direct, indirect, or close contact with infected people via infected respiratory droplets or saliva. Crowded indoor environments with sustained close contact and conversations are a particularly high-risk setting. METHODS We performed a meta-analysis through July 29, 2020 of SARS-CoV-2 household secondary attack rate (SAR), disaggregating by several covariates (contact type, symptom status, adult/child contacts, contact sex, relationship to index case, index case sex, number of contacts in household, coronavirus). FINDINGS We identified 40 relevant published studies that report household secondary transmission. The estimated overall household SAR was 18.8% (95% confidence interval [CI]: 15.4%-22.2%), which is higher than previously observed SARs for SARS-CoV and MERS-CoV. We observed that household SARs were significantly higher from symptomatic index cases than asymptomatic index cases, to adult contacts than children contacts, to spouses than other family contacts, and in households with one contact than households with three or more contacts. INTERPRETATION To prevent the spread of SARS-CoV-2, people are being asked to stay at home worldwide. With suspected or confirmed infections referred to isolate at home, household transmission will continue to be a significant source of transmission.
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Affiliation(s)
| | - Yang Yang
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - Ira M. Longini
- Department of Biostatistics, University of Florida, Gainesville, FL
| | - M. Elizabeth Halloran
- Fred Hutchinson Cancer Research Center, Seattle, WA
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Natalie E. Dean
- Department of Biostatistics, University of Florida, Gainesville, FL
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13
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Grant R, Malik MR, Elkholy A, Van Kerkhove MD. A Review of Asymptomatic and Subclinical Middle East Respiratory Syndrome Coronavirus Infections. Epidemiol Rev 2020; 41:69-81. [PMID: 31781765 PMCID: PMC7108493 DOI: 10.1093/epirev/mxz009] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 04/02/2019] [Accepted: 09/09/2019] [Indexed: 12/14/2022] Open
Abstract
The epidemiology of Middle East respiratory syndrome coronavirus (MERS-CoV) since 2012 has been largely characterized by recurrent zoonotic spillover from dromedary camels followed by limited human-to-human transmission, predominantly in health-care settings. The full extent of infection of MERS-CoV is not clear, nor is the extent and/or role of asymptomatic infections in transmission. We conducted a review of molecular and serological investigations through PubMed and EMBASE from September 2012 to November 15, 2018, to measure subclinical or asymptomatic MERS-CoV infection within and outside of health-care settings. We performed retrospective analysis of laboratory-confirmed MERS-CoV infections reported to the World Health Organization to November 27, 2018, to summarize what is known about asymptomatic infections identified through national surveillance systems. We identified 23 studies reporting evidence of MERS-CoV infection outside of health-care settings, mainly of camel workers, with seroprevalence ranges of 0%–67% depending on the study location. We identified 20 studies in health-care settings of health-care worker (HCW) and family contacts, of which 11 documented molecular evidence of MERS-CoV infection among asymptomatic contacts. Since 2012, 298 laboratory-confirmed cases were reported as asymptomatic to the World Health Organization, 164 of whom were HCWs. The potential to transmit MERS-CoV to others has been demonstrated in viral-shedding studies of asymptomatic MERS infections. Our results highlight the possibility for onward transmission of MERS-CoV from asymptomatic individuals. Screening of HCW contacts of patients with confirmed MERS-CoV is currently recommended, but systematic screening of non-HCW contacts outside of health-care facilities should be encouraged.
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Affiliation(s)
| | | | | | - Maria D Van Kerkhove
- Correspondence to Maria D. Van Kerkhove, PhD, Department of Infectious Hazards Management, Health Emergencies Program, World Health Organization, Avenue Appia 20, 1211 Geneva, Switzerland (e-mail: )
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14
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Tamin A, Queen K, Paden CR, Lu X, Andres E, Sakthivel SK, Li Y, Tao Y, Zhang J, Kamili S, Assiri AM, Alshareef A, Alaifan TA, Altamimi AM, Jokhdar H, Watson JT, Gerber SI, Tong S, Thornburg NJ. Isolation and growth characterization of novel full length and deletion mutant human MERS-CoV strains from clinical specimens collected during 2015. J Gen Virol 2020; 100:1523-1529. [PMID: 31592752 PMCID: PMC7079693 DOI: 10.1099/jgv.0.001334] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Middle East respiratory syndrome (MERS) is a viral respiratory illness first reported in Saudi Arabia in September 2012 caused by the human coronavirus (CoV), MERS-CoV. Using full-genome sequencing and phylogenetic analysis, scientists have identified three clades and multiple lineages of MERS-CoV in humans and the zoonotic host, dromedary camels. In this study, we have characterized eight MERS-CoV isolates collected from patients in Saudi Arabia in 2015. We have performed full-genome sequencing on the viral isolates, and compared them to the corresponding clinical specimens. All isolates were clade B, lineages 4 and 5. Three of the isolates carry deletions located on three independent regions of the genome in the 5'UTR, ORF1a and ORF3. All novel MERS-CoV strains replicated efficiently in Vero and Huh7 cells. Viruses with deletions in the 5'UTR and ORF1a exhibited impaired viral release in Vero cells. These data emphasize the plasticity of the MERS-CoV genome during human infection.
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Affiliation(s)
- Azaibi Tamin
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Krista Queen
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Clinton R Paden
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Xiaoyan Lu
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Erica Andres
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Senthilkumar K Sakthivel
- Batelle, Columbus, OH, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Yan Li
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Ying Tao
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Jing Zhang
- IHRC, Atlanta, GA, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Shifaq Kamili
- IHRC, Atlanta, GA, USA.,National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | | | - Ali Alshareef
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | | | - Asmaa M Altamimi
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | - Hani Jokhdar
- Kingdom of Saudi Arabia Ministry of Health, Riyadh, Saudi Arabia
| | - John T Watson
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Susan I Gerber
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Suxiang Tong
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Division of Viral Diseases, Gastroenteritis and Respiratory Viruses Laboratory Branch, Centers for Disease Control and Prevention (CDC), Atlanta, GA, USA
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15
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Naeem A, Hamed ME, Alghoribi MF, Aljabr W, Alsaran H, Enani MA, Alosaimi B. Molecular Evolution and Structural Mapping of N-Terminal Domain in Spike Gene of Middle East Respiratory Syndrome Coronavirus (MERS-CoV). Viruses 2020; 12:E502. [PMID: 32370153 DOI: 10.3390/v12050502] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/23/2020] [Accepted: 04/29/2020] [Indexed: 01/10/2023] Open
Abstract
The Middle East Respiratory Syndrome Coronavirus (MERS-CoV) is a lethal zoonotic pathogen circulating in the Arabian Peninsula since 2012. There is no vaccine for MERS and anti-viral treatment is generally not applicable. We investigated the evolution of the MERS-CoV spike gene sequences and changes in viral loads over time from patients in Saudi Arabia from 2105-2017. All the MERS-CoV strains belonged to lineage 5, and showed high sequence homology (99.9%) to 2017 strains. Recombination analysis showed a potential recombination event in study strains from patients in Saudi Arabia. The spike gene showed eight amino acid substitutions, especially between the A1 and B5 lineage, and contained positively selected codon 1020. We also determined that the viral loads were significantly (p < 0.001) higher in fatal cases, and virus shedding was prolonged in some fatal cases beyond 21 days. The viral concentration peaked during the first week of illness, and the lower respiratory specimens had higher levels of MERS-CoV RNA. The presence of the diversifying selection and the topologies with the structural mapping of residues under purifying selection suggested that codon 1020 might have a role in the evolution of spike gene during the divergence of different lineages. This study will im-prove our understanding of the evolution of MERS-CoV, and also highlights the need for enhanced surveillance in humans and dromedaries. The presence of amino acid changes at the N-terminal domain and structural mapping of residues under positive selection at heptad repeat 1 provides better insight into the adaptive evolution of the spike gene and might have a potential role in virus-host tropism and pathogenesis.
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Abstract
A new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with human to human transmission and extreme human sickness has been as of late announced from the city of Wuhan in China. Our objectives were to mutation analysis between recently reported genomes at various times and locations and to characterize the genomic structure of SARS-CoV-2 using bioinformatics programs. Information on the variation of viruses is of considerable medical and biological impacts on the prevention, diagnosis, and therapy of infectious diseases. To understand the genomic structure and variations of the SARS-CoV-2. The study analyzed 95 SARS-CoV-2 complete genome sequences available in GenBank, National MicrobiologyData Center (NMDC) and NGDC Genome Warehouse from December-2019 until 05 of April-2020. The genomic signature analysis demonstrates that a strong association between the time of sample collection, location of sample and accumulation of genetic diversity. We found 116 mutations, the three most common mutations were 8782C>T in ORF1ab gene, 28144T>C in ORF8 gene and 29095C>T in the N gene. The mutations might affect the severity and spread of the SARS-CoV-2. The finding heavily supports an intense requirement for additional prompt, inclusive investigations that combine genomic detail, epidemiological information and graph records of the clinical features of patients with COVID-19.
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Key Words
- BLAST, Basic Local Alignment Search Tool
- CDC, Centers of Disease Control and Prevention
- COVID-19
- COVID-19, Coronavirus disease 2019
- EMBOSS, The European Molecular Biology Open Software Suite
- Genomic characterization
- MERS, Middle East Respiratory Syndrome
- Mutation
- NCBI, National Center for Biotechnology Information
- NGDC, National Genomics Data Center
- NMDC, National Microbiology Data Center
- NSP, nonstructural protein
- ORF, Open Reading Frame
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- UTR, Untranslated region
- WHO, World Health Organization
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Affiliation(s)
- Rozhgar A Khailany
- Department of Biology, College of Science, University of Salahaddin-Erbil, Iraq
| | - Muhamad Safdar
- Department of Breeding and Genetics, Cholistan University of Veterinary & Animal Sciences, Bahawalpur 63100, Pakistan
| | - Mehmet Ozaslan
- Department of Biology, Gaziantep University, 27310 Gaziantep, Turkey
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17
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Widagdo W, Sooksawasdi Na Ayudhya S, Hundie GB, Haagmans BL. Host Determinants of MERS-CoV Transmission and Pathogenesis. Viruses 2019; 11:E280. [PMID: 30893947 PMCID: PMC6466079 DOI: 10.3390/v11030280] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/11/2019] [Accepted: 03/13/2019] [Indexed: 01/01/2023] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a zoonotic pathogen that causes respiratory infection in humans, ranging from asymptomatic to severe pneumonia. In dromedary camels, the virus only causes a mild infection but it spreads efficiently between animals. Differences in the behavior of the virus observed between individuals, as well as between humans and dromedary camels, highlight the role of host factors in MERS-CoV pathogenesis and transmission. One of these host factors, the MERS-CoV receptor dipeptidyl peptidase-4 (DPP4), may be a critical determinant because it is variably expressed in MERS-CoV-susceptible species as well as in humans. This could partially explain inter- and intraspecies differences in the tropism, pathogenesis, and transmissibility of MERS-CoV. In this review, we explore the role of DPP4 and other host factors in MERS-CoV transmission and pathogenesis-such as sialic acids, host proteases, and interferons. Further characterization of these host determinants may potentially offer novel insights to develop intervention strategies to tackle ongoing outbreaks.
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Affiliation(s)
- W Widagdo
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | | | - Gadissa B Hundie
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, The Netherlands.
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18
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Alanazi KH, Killerby ME, Biggs HM, Abedi GR, Jokhdar H, Alsharef AA, Mohammed M, Abdalla O, Almari A, Bereagesh S, Tawfik S, Alresheedi H, Alhakeem RF, Hakawi A, Alfalah H, Amer H, Thornburg NJ, Tamin A, Trivedi S, Tong S, Lu X, Queen K, Li Y, Sakthivel SK, Tao Y, Zhang J, Paden CR, Al-Abdely HM, Assiri AM, Gerber SI, Watson JT. Scope and extent of healthcare-associated Middle East respiratory syndrome coronavirus transmission during two contemporaneous outbreaks in Riyadh, Saudi Arabia, 2017. Infect Control Hosp Epidemiol 2019; 40:79-88. [PMID: 30595141 PMCID: PMC7108661 DOI: 10.1017/ice.2018.290] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/16/2018] [Indexed: 12/29/2022]
Abstract
OBJECTIVE To investigate a Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak event involving multiple healthcare facilities in Riyadh, Saudi Arabia; to characterize transmission; and to explore infection control implications. DESIGN Outbreak investigation. SETTING Cases presented in 4 healthcare facilities in Riyadh, Saudi Arabia: a tertiary-care hospital, a specialty pulmonary hospital, an outpatient clinic, and an outpatient dialysis unit. METHODS Contact tracing and testing were performed following reports of cases at 2 hospitals. Laboratory results were confirmed by real-time reverse transcription polymerase chain reaction (rRT-PCR) and/or genome sequencing. We assessed exposures and determined seropositivity among available healthcare personnel (HCP) cases and HCP contacts of cases. RESULTS In total, 48 cases were identified, involving patients, HCP, and family members across 2 hospitals, an outpatient clinic, and a dialysis clinic. At each hospital, transmission was linked to a unique index case. Moreover, 4 cases were associated with superspreading events (any interaction where a case patient transmitted to ≥5 subsequent case patients). All 4 of these patients were severely ill, were initially not recognized as MERS-CoV cases, and subsequently died. Genomic sequences clustered separately, suggesting 2 distinct outbreaks. Overall, 4 (24%) of 17 HCP cases and 3 (3%) of 114 HCP contacts of cases were seropositive. CONCLUSIONS We describe 2 distinct healthcare-associated outbreaks, each initiated by a unique index case and characterized by multiple superspreading events. Delays in recognition and in subsequent implementation of control measures contributed to secondary transmission. Prompt contact tracing, repeated testing, HCP furloughing, and implementation of recommended transmission-based precautions for suspected cases ultimately halted transmission.
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Affiliation(s)
| | - Marie E. Killerby
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
- King Saud Medical City, Riyadh, Saudi Arabia
| | - Holly M. Biggs
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Glen R. Abedi
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | | | | | | | | | | | | | | | | | | | | | | | - Hala Amer
- King Saud Medical City, Riyadh, Saudi Arabia
- Department of Community Medicine, National Research Center, Cairo, Egypt
| | - Natalie J. Thornburg
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Azaibi Tamin
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Suvang Trivedi
- IHRC, contractor to National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Suxiang Tong
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Xiaoyan Lu
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Krista Queen
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Yan Li
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Senthilkumar K. Sakthivel
- Batelle, contractor to National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ying Tao
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Jing Zhang
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - Clinton R. Paden
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | | | | | - Susan I. Gerber
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
| | - John T. Watson
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States
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