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Pierce JB, Simion V, Icli B, Pérez-Cremades D, Cheng HS, Feinberg MW. Computational Analysis of Targeting SARS-CoV-2, Viral Entry Proteins ACE2 and TMPRSS2, and Interferon Genes by Host MicroRNAs. Genes (Basel) 2020; 11:E1354. [PMID: 33207533 PMCID: PMC7696723 DOI: 10.3390/genes11111354] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2020] [Revised: 10/16/2020] [Accepted: 10/16/2020] [Indexed: 01/18/2023] Open
Abstract
Rapid spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), has led to a global pandemic, failures of local health care systems, and global economic recession. MicroRNAs (miRNAs) have recently emerged as important regulators of viral pathogenesis, particularly among RNA viruses, but the impact of host miRNAs on SARS-CoV-2 infectivity remains unknown. In this study, we utilize the combination of powerful bioinformatic prediction algorithms and miRNA profiling to predict endogenous host miRNAs that may play important roles in regulating SARS-CoV-2 infectivity. We provide a collection of high-probability miRNA binding sites within the SARS-CoV-2 genome as well as within mRNA transcripts of critical viral entry proteins ACE2 and TMPRSS2 and their upstream modulators, the interferons (IFN). By utilizing miRNA profiling datasets of SARS-CoV-2-resistant and -susceptible cell lines, we verify the biological plausibility of the predicted miRNA-target RNA interactions. Finally, we utilize miRNA profiling of SARS-CoV-2-infected cells to identify predicted miRNAs that are differentially regulated in infected cells. In particular, we identify predicted miRNA binders to SARS-CoV-2 ORFs (miR-23a (1ab), miR-29a, -29c (1ab, N), miR-151a, -151b (S), miR-4707-3p (S), miR-298 (5'-UTR), miR-7851-3p (5'-UTR), miR-8075 (5'-UTR)), ACE2 3'-UTR (miR-9-5p, miR-218-5p), TMPRSS2 3'-UTR (let-7d-5p, -7e-5p, miR-494-3p, miR-382-3p, miR-181c-5p), and IFN-α 3'-UTR (miR-361-5p, miR-410-3p). Overall, this study provides insight into potential novel regulatory mechanisms of SARS-CoV-2 by host miRNAs and lays the foundation for future investigation of these miRNAs as potential therapeutic targets or biomarkers.
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Affiliation(s)
- Jacob B. Pierce
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
- Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Viorel Simion
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Basak Icli
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Daniel Pérez-Cremades
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Henry S. Cheng
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
| | - Mark W. Feinberg
- Department of Medicine, Cardiovascular Division, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA 02115, USA; (J.B.P.); (V.S.); (B.I.); (D.P.-C.); (H.S.C.)
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52
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Naidu SAG, Clemens RA, Pressman P, Zaigham M, Davies KJA, Naidu AS. COVID-19 during Pregnancy and Postpartum. J Diet Suppl 2020; 19:78-114. [PMID: 33164606 DOI: 10.1080/19390211.2020.1834047] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
As the COVID-19 pandemic intensified the global health crisis, the containment of SARS-CoV-2 infection in pregnancies, and the inherent risk of vertical transmission of virus from mother-to-fetus (or neonate) poses a major concern. Most COVID-19-Pregnancy patients showed mild to moderate COVID-19 pneumonia with no pregnancy loss and no congenital transmission of the virus; however, an increase in hypoxia-induced preterm deliveries was apparent. Also, the breastmilk of several mothers with COVID-19 tested negative for the virus. Taken together, the natural barrier function during pregnancy and postpartum seems to deter the SARS-CoV-2 transmission from mother-to-child. This clinical observation warrants to explore the maternal-fetal interface and identify the innate defense factors for prevention and control of COVID-19-Pregnancy. Lactoferrin (LF) is a potent antiviral iron-binding protein present in the maternal-fetal interface. In concert with immune co-factors, maternal-LF modulates chemokine release and lymphocyte migration and amplify host defense during pregnancy. LF levels during pregnancy may resolve hypertension via down-regulation of ACE2; consequently, may limit the membrane receptor access to SARS-CoV-2 for cellular entry. Furthermore, an LF-derived peptide (LRPVAA) has been shown to block ACE receptor activity in vitro. LF may also reduce viral docking and entry into host cells and limit the early phase of COVID-19 infection. An in-depth understanding of LF and other soluble mammalian milk-derived innate antiviral factors may provide insights to reduce co-morbidities and vertical transmission of SARS-CoV-2 infection and may lead to the development of effective nutraceutical supplements.
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Affiliation(s)
| | - Roger A Clemens
- School of Pharmacy, University of Southern California, Los Angeles, CA, USA
| | | | - Mehreen Zaigham
- Department of Obstetrics & Gynecology, Skåne University Hospital, Malmö, Sweden
| | - Kelvin J A Davies
- Division of Biogerontology, Leonard Davis School of Gerontology, The University of Southern California, Los Angeles, CA, USA.,Division of Molecular & Computational Biology, Dornsife College of Letters, Arts, and Sciences, The University of Southern California, Los Angeles, CA, USA.,Department Biochemistry & Molecular Medicine, Keck School of Medicine of USC, The University of Southern California, Los Angeles, CA, USA
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53
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Escalera-Zamudio M, Golden M, Gutiérrez B, Thézé J, Keown JR, Carrique L, Bowden TA, Pybus OG. Parallel evolution in the emergence of highly pathogenic avian influenza A viruses. Nat Commun 2020; 11:5511. [PMID: 33139731 PMCID: PMC7608645 DOI: 10.1038/s41467-020-19364-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/12/2020] [Indexed: 01/30/2023] Open
Abstract
Parallel molecular evolution and adaptation are important phenomena commonly observed in viruses. Here, we exploit parallel molecular evolution to understand virulence evolution in avian influenza viruses (AIV). Highly-pathogenic AIVs evolve independently from low-pathogenic ancestors via acquisition of polybasic cleavage sites. Why some AIV lineages but not others evolve in this way is unknown. We hypothesise that the parallel emergence of highly-pathogenic AIV may be facilitated by permissive or compensatory mutations occurring across the viral genome. We combine phylogenetic, statistical and structural approaches to discover parallel mutations in AIV genomes associated with the highly-pathogenic phenotype. Parallel mutations were screened using a statistical test of mutation-phenotype association and further evaluated in the contexts of positive selection and protein structure. Our resulting mutational panel may help to reveal new links between virulence evolution and other traits, and raises the possibility of predicting aspects of AIV evolution.
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Affiliation(s)
| | - Michael Golden
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | | | - Julien Thézé
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK
| | - Jeremy Russell Keown
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Loic Carrique
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Thomas A Bowden
- Division of Structural Biology, Wellcome Centre for Human Genetics, Oxford, OX3 7BN, UK
| | - Oliver G Pybus
- Department of Zoology, Oxford University, Parks Rd, Oxford, OX1 3PS, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, UK.
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54
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Kirtipal N, Bharadwaj S, Kang SG. From SARS to SARS-CoV-2, insights on structure, pathogenicity and immunity aspects of pandemic human coronaviruses. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2020; 85:104502. [PMID: 32798769 PMCID: PMC7425554 DOI: 10.1016/j.meegid.2020.104502] [Citation(s) in RCA: 153] [Impact Index Per Article: 38.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023]
Abstract
Human Coronaviruses (HCoV), periodically emerging across the world, are potential threat to humans such as severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) - diseases termed as COVID-19. Current SARS-CoV-2 outbreak have fueled ongoing efforts to exploit various viral target proteins for therapy, but strategies aimed at blocking the viral proteins as in drug and vaccine development have largely failed. In fact, evidence has now shown that coronaviruses undergoes rapid recombination to generate new strains of altered virulence; additionally, escaped the host antiviral defense system and target humoral immune system which further results in severe deterioration of the body such as by cytokine storm. This demands the understanding of phenotypic and genotypic classification, and pathogenesis of SARS-CoV-2 for the production of potential therapy. In lack of clear clinical evidences for the pathogenesis of COVID-19, comparative analysis of previous pandemic HCoVs associated immunological responses can provide insights into COVID-19 pathogenesis. In this review, we summarize the possible origin and transmission mode of CoVs and the current understanding on the viral genome integrity of known pandemic virus against SARS-CoV-2. We also consider the host immune response and viral evasion based on available clinical evidences which would be helpful to remodel COVID-19 pathogenesis; and hence, development of therapeutics against broad spectrum of coronaviruses.
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Affiliation(s)
- Nikhil Kirtipal
- Department of Science, Modern Institute of Technology, Dhalwala, Rishikesh, Uttarakhand, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, 280 Daehak-Ro, Gyeongsan, Gyeongbuk 38541, Republic of Korea.
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55
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The Effects of Genetic Variation on H7N9 Avian Influenza Virus Pathogenicity. Viruses 2020; 12:v12111220. [PMID: 33126529 PMCID: PMC7693985 DOI: 10.3390/v12111220] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 10/18/2020] [Accepted: 10/26/2020] [Indexed: 12/12/2022] Open
Abstract
Since the H7N9 avian influenza virus emerged in China in 2013, there have been five seasonal waves which have shown human infections and caused high fatality rates in infected patients. A multibasic amino acid insertion seen in the HA of current H7N9 viruses occurred through natural evolution and reassortment, and created a high pathogenicity avian influenza (HPAI) virus from the low pathogenicity avian influenza (LPAI) in 2017, and significantly increased pathogenicity in poultry, resulting in widespread HPAI H7N9 in poultry, which along with LPAI H7N9, contributed to the severe fifth seasonal wave in China. H7N9 is a novel reassorted virus from three different subtypes of influenza A viruses (IAVs) which displays a great potential threat to public health and the poultry industry. To date, no sustained human-to-human transmission has been recorded by the WHO. However, the high ability of evolutionary adaptation of H7N9 and lack of pre-existing immunity in humans heightens the pandemic potential. Changes in IAVs proteins can affect the viral transmissibility, receptor binding specificity, pathogenicity, and virulence. The multibasic amino acid insertion, mutations in hemagglutinin, deletion and mutations in neuraminidase, and mutations in PB2 contribute to different virological characteristics. This review summarized the latest research evidence to describe the impacts of viral protein changes in viral adaptation and pathogenicity of H7N9, aiming to provide better insights for developing and enhancing early warning or intervention strategies with the goal of preventing highly pathogenic IAVs circulation in live poultry, and transmission to humans.
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56
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Örd M, Faustova I, Loog M. The sequence at Spike S1/S2 site enables cleavage by furin and phospho-regulation in SARS-CoV2 but not in SARS-CoV1 or MERS-CoV. Sci Rep 2020; 10:16944. [PMID: 33037310 PMCID: PMC7547067 DOI: 10.1038/s41598-020-74101-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Accepted: 09/25/2020] [Indexed: 12/22/2022] Open
Abstract
The Spike protein of the novel coronavirus SARS-CoV2 contains an insertion 680SPRRAR↓SV687 forming a cleavage motif RxxR for furin-like enzymes at the boundary of S1/S2 subunits. Cleavage at S1/S2 is important for efficient viral entry into target cells. The insertion is absent in other CoV-s of the same clade, including SARS-CoV1 that caused the 2003 outbreak. However, an analogous cleavage motif was present at S1/S2 of the Spike protein of the more distant Middle East Respiratory Syndrome coronavirus MERS-CoV. We show that a crucial third arginine at the left middle position, comprising a motif RRxR is required for furin recognition in vitro, while the general motif RxxR in common with MERS-CoV is not sufficient for cleavage. Further, we describe a surprising finding that the two serines at the edges of the insert SPRRAR↓SV can be efficiently phosphorylated by proline-directed and basophilic protein kinases. Both phosphorylations switch off furin’s ability to cleave the site. Although phospho-regulation of secreted proteins is still poorly understood, further studies, supported by a recent report of ten in vivo phosphorylated sites in the Spike protein of SARS-CoV2, could potentially uncover important novel regulatory mechanisms for SARS-CoV2.
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Affiliation(s)
- Mihkel Örd
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Ilona Faustova
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia
| | - Mart Loog
- Institute of Technology, University of Tartu, 50411, Tartu, Estonia.
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57
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Emergence of highly pathogenic H5N2 and H7N1 influenza A viruses from low pathogenic precursors by serial passage in ovo. PLoS One 2020; 15:e0240290. [PMID: 33031421 PMCID: PMC7544131 DOI: 10.1371/journal.pone.0240290] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/24/2020] [Indexed: 02/01/2023] Open
Abstract
Highly pathogenic (HPAI) strains emerge from their low pathogenic (LPAI) precursors and cause severe disease in poultry with enormous economic losses, and zoonotic potential. Understanding the mechanisms involved in HPAI emergence is thus an important goal for risk assessments. In this study ostrich-origin H5N2 and H7N1 LPAI progenitor viruses were serially passaged seventeen times in 14-day old embryonated chicken eggs and Ion Torrent ultra-deep sequencing was used to monitor the incremental changes in the consensus genome sequences. Both virus strains increased in virulence with successive passages, but the H7N1 virus attained a virulent phenotype sooner. Mutations V63M, E228V and D272G in the HA protein, Q357K in the nucleoprotein (NP) and H155P in the neuraminidase protein correlated with the increased pathogenicity of the H5N2 virus; whereas R584H and L589I substitutions in the polymerase B2 protein, A146T and Q220E in HA plus D231N in the matrix 1 protein correlated with increased pathogenicity of the H7N1 virus in embryos. Enzymatic cleavage of HA protein is the critical virulence determinant, and HA cleavage site motifs containing multibasic amino acids were detected at the sub-consensus level. The motifs PQERRR/GLF and PQRERR/GLF were first detected in passages 11 and 15 respectively of the H5N2 virus, and in the H7N1 virus the motifs PELPKGKK/GLF and PELPKRR/GLF were detected as early as passage 7. Most significantly, a 13 nucleotide insert of unknown origin was identified at passage 6 of the H5N2 virus, and at passage 17 a 42 nucleotide insert derived from the influenza NP gene was identified. This is the first report of non-homologous recombination at the HA cleavage site in an H5 subtype virus. This study provides insights into how HPAI viruses emerge from low pathogenic precursors and demonstrated the pathogenic potential of H5N2 and H7N1 strains that have not yet been implicated in HPAI outbreaks.
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58
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Lemmin T, Kalbermatter D, Harder D, Plattet P, Fotiadis D. Structures and dynamics of the novel S1/S2 protease cleavage site loop of the SARS-CoV-2 spike glycoprotein. JOURNAL OF STRUCTURAL BIOLOGY-X 2020; 4:100038. [PMID: 33043289 PMCID: PMC7534663 DOI: 10.1016/j.yjsbx.2020.100038] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/23/2020] [Accepted: 09/30/2020] [Indexed: 01/12/2023]
Abstract
At the end of 2019, a new highly virulent coronavirus known under the name SARS-CoV-2 emerged as a human pathogen. One key feature of SARS-CoV-2 is the presence of an enigmatic insertion in the spike glycoprotein gene representing a novel multibasic S1/S2 protease cleavage site. The proteolytic cleavage of the spike at this site is essential for viral entry into host cells. However, it has been systematically abrogated in structural studies in order to stabilize the spike in the prefusion state. In this study, multi-microsecond molecular dynamics simulations and ab initio modeling were leveraged to gain insights into the structures and dynamics of the loop containing the S1/S2 protease cleavage site. They unveiled distinct conformations, formations of short helices and interactions of the loop with neighboring glycans that could potentially regulate the accessibility of the cleavage site to proteases and its processing. In most conformations, this loop protrudes from the spike, thus representing an attractive SARS-CoV-2 specific therapeutic target.
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Affiliation(s)
- Thomas Lemmin
- DS3Lab, System Group, Department of Computer Sciences, ETH Zurich, CH-8092 Zürich, Switzerland.,Trkola Group, Institute for Virology, University of Zurich, CH-8057 Zürich, Switzerland
| | - David Kalbermatter
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland
| | - Daniel Harder
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland
| | - Philippe Plattet
- Division of Experimental and Clinical Research, Vetsuisse Faculty, University of Bern, CH-3012 Bern, Switzerland
| | - Dimitrios Fotiadis
- Institute of Biochemistry and Molecular Medicine, and Swiss National Centre of Competence in Research (NCCR) TransCure, University of Bern, CH-3012 Bern, Switzerland
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59
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Elrashdy F, Redwan EM, Uversky VN. Why COVID-19 Transmission Is More Efficient and Aggressive Than Viral Transmission in Previous Coronavirus Epidemics? Biomolecules 2020; 10:E1312. [PMID: 32933047 PMCID: PMC7565143 DOI: 10.3390/biom10091312] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 09/08/2020] [Indexed: 12/19/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is causing a pandemic of coronavirus disease 2019 (COVID-19). The worldwide transmission of COVID-19 from human to human is spreading like wildfire, affecting almost every country in the world. In the past 100 years, the globe did not face a microbial pandemic similar in scale to COVID-19. Taken together, both previous outbreaks of other members of the coronavirus family (severe acute respiratory syndrome (SARS-CoV) and middle east respiratory syndrome (MERS-CoV)) did not produce even 1% of the global harm already inflicted by COVID-19. There are also four other CoVs capable of infecting humans (HCoVs), which circulate continuously in the human population, but their phenotypes are generally mild, and these HCoVs received relatively little attention. These dramatic differences between infection with HCoVs, SARS-CoV, MERS-CoV, and SARS-CoV-2 raise many questions, such as: Why is COVID-19 transmitted so quickly? Is it due to some specific features of the viral structure? Are there some specific human (host) factors? Are there some environmental factors? The aim of this review is to collect and concisely summarize the possible and logical answers to these questions.
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Affiliation(s)
- Fatma Elrashdy
- Department of Endemic Medicine and Hepatogastroenterology, Kasr Alainy School of Medicine, Cairo University, Cairo 11562, Egypt;
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
| | - Vladimir N. Uversky
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Pushchino, 142290 Moscow, Russia
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Kalonda A, Saasa N, Nkhoma P, Kajihara M, Sawa H, Takada A, Simulundu E. Avian Influenza Viruses Detected in Birds in Sub-Saharan Africa: A Systematic Review. Viruses 2020; 12:v12090993. [PMID: 32906666 PMCID: PMC7552061 DOI: 10.3390/v12090993] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/03/2020] [Accepted: 09/05/2020] [Indexed: 12/20/2022] Open
Abstract
In the recent past, sub-Saharan Africa has not escaped the devastating effects of avian influenza virus (AIV) in poultry and wild birds. This systematic review describes the prevalence, spatiotemporal distribution, and virus subtypes detected in domestic and wild birds for the past two decades (2000–2019). We collected data from three electronic databases, PubMed, SpringerLink electronic journals and African Journals Online, using the Preferred Reporting Items for Systematic reviews and Meta-Analyses protocol. A total of 1656 articles were reviewed, from which 68 were selected. An overall prevalence of 3.0% AIV in birds was observed. The prevalence varied between regions and ranged from 1.1% to 7.1%. The Kruskal–Wallis and Wilcoxon signed-rank sum test showed no significant difference in the prevalence of AIV across regions, χ2(3) = 5.237, p = 0.1553 and seasons, T = 820, z = −1.244, p = 0.2136. Nineteen hemagglutinin/neuraminidase subtype combinations were detected during the reviewed period, with southern Africa recording more diverse AIV subtypes than other regions. The most detected subtype was H5N1, followed by H9N2, H5N2, H5N8 and H6N2. Whilst these predominant subtypes were mostly detected in domestic poultry, H1N6, H3N6, H4N6, H4N8, H9N1 and H11N9 were exclusively detected in wild birds. Meanwhile, H5N1, H5N2 and H5N8 were detected in both wild and domestic birds suggesting circulation of these subtypes among wild and domestic birds. Our findings provide critical information on the eco-epidemiology of AIVs that can be used to improve surveillance strategies for the prevention and control of avian influenza in sub-Saharan Africa.
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Affiliation(s)
- Annie Kalonda
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Africa Centre of Excellence for Infectious Disease of Humans and Animals, School of Veterinary Medicine, Lusaka 10101, Zambia
| | - Ngonda Saasa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
| | - Panji Nkhoma
- Department of Biomedical Sciences, School of Health Sciences, University of Zambia, Lusaka 10101, Zambia; (A.K.); (P.N.)
| | - Masahiro Kajihara
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Research Center for Zoonosis Control, Hokkaido University, Sapporo 001-0020, Japan;
- Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University Kita-ku, Sapporo 001-0020, Japan
| | - Edgar Simulundu
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, Lusaka 10101, Zambia; (N.S.); (H.S.); (A.T.)
- Macha Research Trust, Choma 20100, Zambia
- Correspondence: ; Tel.: +260-977469479
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61
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Flores-Alanis A, Sandner-Miranda L, Delgado G, Cravioto A, Morales-Espinosa R. The receptor binding domain of SARS-CoV-2 spike protein is the result of an ancestral recombination between the bat-CoV RaTG13 and the pangolin-CoV MP789. BMC Res Notes 2020; 13:398. [PMID: 32854762 PMCID: PMC7450963 DOI: 10.1186/s13104-020-05242-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/19/2020] [Indexed: 12/24/2022] Open
Abstract
OBJECTIVE In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.
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Affiliation(s)
- Alejandro Flores-Alanis
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luisa Sandner-Miranda
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriela Delgado
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Cravioto
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Seekings AH, Howard WA, Nuñéz A, Slomka MJ, Banyard AC, Hicks D, Ellis RJ, Nuñéz-García J, Hartgroves LC, Barclay WS, Banks J, Brown IH. The Emergence of H7N7 Highly Pathogenic Avian Influenza Virus from Low Pathogenicity Avian Influenza Virus Using an in ovo Embryo Culture Model. Viruses 2020; 12:v12090920. [PMID: 32839404 PMCID: PMC7552004 DOI: 10.3390/v12090920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/15/2020] [Accepted: 08/18/2020] [Indexed: 01/19/2023] Open
Abstract
Outbreaks of highly pathogenic avian influenza virus (HPAIV) often result in the infection of millions of poultry, causing up to 100% mortality. HPAIV has been shown to emerge from low pathogenicity avian influenza virus (LPAIV) in field outbreaks. Direct evidence for the emergence of H7N7 HPAIV from a LPAIV precursor with a rare di-basic cleavage site (DBCS) was identified in the UK in 2008. The DBCS contained an additional basic amino acid compared to commonly circulating LPAIVs that harbor a single-basic amino acid at the cleavage site (SBCS). Using reverse genetics, outbreak HPAIVs were rescued with a DBCS (H7N7DB), as seen in the LPAIV precursor or an SBCS representative of common H7 LPAIVs (H7N7SB). Passage of H7N7DB in chicken embryo tissues showed spontaneous evolution to a HPAIV. In contrast, deep sequencing of extracts from embryo tissues in which H7N7SB was serially passaged showed retention of the LPAIV genotype. Thus, in chicken embryos, an H7N7 virus containing a DBCS appears naturally unstable, enabling rapid evolution to HPAIV. Evaluation in embryo tissue presents a useful approach to study AIV evolution and allows a laboratory-based dissection of molecular mechanisms behind the emergence of HPAIV.
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Affiliation(s)
- Amanda H. Seekings
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
- Correspondence:
| | - Wendy A. Howard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Alejandro Nuñéz
- Pathology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (A.N.); (D.H.)
| | - Marek J. Slomka
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Ashley C. Banyard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
- School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QG, UK
- Institute for Infection and Immunity, St. George’s Hospital Medical School, University of London, London SW17 0RE, UK
| | - Daniel Hicks
- Pathology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (A.N.); (D.H.)
| | - Richard J. Ellis
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (R.J.E.); (J.N.-G.)
| | - Javier Nuñéz-García
- Surveillance and Laboratory Services Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (R.J.E.); (J.N.-G.)
| | | | - Wendy S. Barclay
- Virology Department, Imperial College, London W2 1NY, UK; (L.C.H.); (W.S.B.)
| | - Jill Banks
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
| | - Ian H. Brown
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, UK; (W.A.H.); (M.J.S.); (A.C.B.); (J.B.); (I.H.B.)
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63
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Sirotkin K, Sirotkin D. Might SARS-CoV-2 Have Arisen via Serial Passage through an Animal Host or Cell Culture?: A potential explanation for much of the novel coronavirus' distinctive genome. Bioessays 2020; 42:e2000091. [PMID: 32786014 PMCID: PMC7435492 DOI: 10.1002/bies.202000091] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 07/13/2020] [Indexed: 12/16/2022]
Abstract
Despite claims from prominent scientists that SARS-CoV-2 indubitably emerged naturally, the etiology of this novel coronavirus remains a pressing and open question: Without knowing the true nature of a disease, it is impossible for clinicians to appropriately shape their care, for policy-makers to correctly gauge the nature and extent of the threat, and for the public to appropriately modify their behavior. Unless the intermediate host necessary for completing a natural zoonotic jump is identified, the dual-use gain-of-function research practice of viral serial passage should be considered a viable route by which the novel coronavirus arose. The practice of serial passage mimics a natural zoonotic jump, and offers explanations for SARS-CoV-2's distinctive spike-protein region and its unexpectedly high affinity for angiotensin converting enzyme (ACE2), as well as the notable polybasic furin cleavage site within it. Additional molecular clues raise further questions, all of which warrant full investigation into the novel coronavirus's origins and a re-examination of the risks and rewards of dual-use gain-of-function research.
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Affiliation(s)
- Karl Sirotkin
- Karl Sirotkin LLC, 1301 Tadsworth Terrace, Lake Mary, FL, 32746, USA
| | - Dan Sirotkin
- Karl Sirotkin LLC, 1301 Tadsworth Terrace, Lake Mary, FL, 32746, USA
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64
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Zhang M, Zhao C, Chen H, Teng Q, Jiang L, Feng D, Li X, Yuan S, Xu J, Zhang X, Li Z. Internal Gene Cassette From a Human-Origin H7N9 Influenza Virus Promotes the Pathogenicity of H9N2 Avian Influenza Virus in Mice. Front Microbiol 2020; 11:1441. [PMID: 32793127 PMCID: PMC7387514 DOI: 10.3389/fmicb.2020.01441] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 06/04/2020] [Indexed: 12/01/2022] Open
Abstract
H9N2 avian influenza virus is one of the most widely circulating viruses in poultry and poses a huge potential threat to human health due to its frequent gene reassortment with other influenza viruses. In this study, we generated a series of H9N2-H7N9 reassortant viruses and examined their pathogenicity in a mouse model. We found that HA or combined HA and NA replacement on the H9N2 background led to no substantial change in the virus-induced pathogenicity, whereas H9N2 virus containing H7N9 internal genes had significantly higher virulence in comparison to the parental H9N2 virus. This increased pathogenicity is associated with enhanced viral replication both in mice and in MDCK cells. We further demonstrated that the viral ribonucleoprotein complex from H7N9 virus possessed higher activity than that from its H9N2 counterpart. Collectively, our data demonstrated that genetic compatibility between H9N2 and H7N9 viruses facilitated the reassortment between H7N9 and H9N2 viruses co-circulated in poultry and that internal gene replacement would convert H9N2 virus into a novel threat to human health.
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Affiliation(s)
- Miaomiao Zhang
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China.,Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chen Zhao
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
| | - Qiaoyang Teng
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
| | - Lang Jiang
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Daobin Feng
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xuesong Li
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
| | - Songhua Yuan
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianqing Xu
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaoyan Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center & Institutes of Biomedical Sciences, Key Laboratory of Medical Molecular Virology of Ministry of Education/Health, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zejun Li
- Shanghai Veterinary Research Institute, Chinese Academic of Agricultural Sciences & Animal Influenza Virus Evolution and Pathogenesis Innovation Team of the Agricultural Science and Technology Innovation Team, Shanghai, China
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65
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Ciotti M, Ciccozzi M, Terrinoni A, Jiang WC, Wang CB, Bernardini S. The COVID-19 pandemic. Crit Rev Clin Lab Sci 2020; 57:365-388. [DOI: 10.1080/10408363.2020.1783198] [Citation(s) in RCA: 114] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Marco Ciotti
- Virology Unit, Tor Vergata University Covid-Hospital, Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, Italy
| | | | - Wen-Can Jiang
- Department of Laboratory Medicine, Chinese PLA General Hospital, Beijing, China
| | - Cheng-Bin Wang
- Department of Laboratory Medicine, Chinese PLA General Hospital, Beijing, China
| | - Sergio Bernardini
- Department of Experimental Medicine, University of Tor Vergata, Rome, Italy
- Emerging Technologies Division, International Federation of Clinical Chemistry and Laboratory Medicine (IFCC), Milano, Italy
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66
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Proteolytic Cleavage of the SARS-CoV-2 Spike Protein and the Role of the Novel S1/S2 Site. iScience 2020; 23:101212. [PMID: 32512386 PMCID: PMC7255728 DOI: 10.1016/j.isci.2020.101212] [Citation(s) in RCA: 220] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 05/04/2020] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread to the entire world within a few months. The origin of SARS-CoV-2 has been related to the lineage B Betacoronavirus SARS-CoV and SARS-related coronaviruses found in bats. Early characterizations of the SARS-CoV-2 genome revealed the existence of a distinct four amino acid insert within the spike (S) protein (underlined, SPRRAR↓S), at the S1/S2 site located at the interface between the S1 receptor binding subunit and the S2 fusion subunit. Notably, this insert appears to be a distinguishing feature among SARS-related sequences and introduces a potential cleavage site for the protease furin. Here, we investigate the potential role of this novel S1/S2 cleavage site and present direct biochemical evidence for proteolytic processing by a variety of proteases. We discuss these findings in the context of the origin of SARS-CoV-2, viral stability, and transmission.
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67
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Abstract
The emergence and rapid global spread of SARS-CoV-2 mark the third such identification of a novel coronavirus capable of causing severe, potentially fatal disease in humans in the 21st century. As noted by Andersen et al. (Nature Medicine), the sequencing of proximal zoonotic ancestors to SARS-CoV-2 has aided in the identification of alleles that may contribute to the virus’ virulence in humans.
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Affiliation(s)
- Rachel L Graham
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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68
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Jaimes JA, Millet JK, Whittaker GR. Proteolytic cleavage of the SARS-CoV-2 spike protein and the role of the novel S1/S2 site. SSRN 2020:3581359. [PMID: 32714113 PMCID: PMC7366798 DOI: 10.2139/ssrn.3581359] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 05/07/2020] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 19 (COVID-19) has rapidly spread from an initial outbreak in Wuhan, China in December 2019 to the rest of the world within a few months. On March 11th 2020, the rapidly evolving COVID-19 situation was characterized as a pandemic by the WHO. Much attention has been drawn to the origin of SARS-CoV-2, a virus which is related to the lineage B betacoronavirus SARS-CoV and SARS-related coronaviruses found in bat species. The closest known relative to SARS-CoV-2 is a bat coronavirus named RaTG13 (BatCoV-RaTG13). Early characterizations of the SARS-CoV-2 genome revealed the existence of a distinct 4 amino acid insert (underlined, SPRRAR↓S), found within the spike (S) protein, at a position termed the S1/S2 site located at the interface between the S1 receptor binding subunit and the S2 fusion subunit. Notably, this S1/S2 insert appears to be distinguishing feature among SARS-related sequences and introduces a potential cleavage site for the protease furin. Here, we investigate the potential role of this novel S1/S2 cleavage site and present direct biochemical evidence for proteolytic processing by a variety of proteases, including furin, trypsin-like proteases and cathepsins. We discuss these findings in the broader context of the origin of SARS-CoV-2, viral stability and transmission.
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Affiliation(s)
- Javier A Jaimes
- Department of Microbiology & Immunology, Cornell University, Ithaca NY 14853, United States
| | - Jean K Millet
- Université Paris-Saclay, INRAE, UVSQ, Virologie et Immunologie Moléculaires, 78352 Jouy-en-Josas, France
| | - Gary R Whittaker
- Department of Microbiology & Immunology, Cornell University, Ithaca NY 14853, United States
- Master of Public Health Program, Cornell University, Ithaca NY 14853, United States
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69
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Affiliation(s)
- Kristian G Andersen
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- Scripps Research Translational Institute, La Jolla, CA, USA.
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - W Ian Lipkin
- Center for Infection and Immunity, Mailman School of Public Health of Columbia University, New York, NY, USA
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, Australia
| | - Robert F Garry
- Tulane University, School of Medicine, Department of Microbiology and Immunology, New Orleans, LA, USA
- Zalgen Labs, Germantown, MD, USA
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70
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Anand K, Karade S, Sen S, Gupta R. SARS-CoV-2: Camazotz's Curse. Med J Armed Forces India 2020; 76:136-141. [PMID: 32341622 PMCID: PMC7183968 DOI: 10.1016/j.mjafi.2020.04.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 04/22/2020] [Indexed: 02/08/2023] Open
Abstract
The world is currently face to face with a pandemic which is spreading rapidly across the globe caused by SARS-CoV-2, a strain of Coronaviruses (CoVs) belonging to subgenus Sarbecovirus of genus Betacoronavirus. World Health Organisation (WHO) on 11 Feb 20 named this disease caused by SARS-CoV-2 as Covid-19. This pandemic is spreading rapidly and more than 20,00,000 cases have occurred globally. The human Coronaviruses discovered in 1960s were considered potentially harmless endemic viruses with seasonal distribution before late 2002. The CoVs are found in a large number of domestic and wild animals and birds. The first pandemic caused by Coronavirus caused by SARS-CoV was recognized in the late 2002 in Guangdong Province and resulted in widespread morbidity and mortality. This was followed by MERS-CoV which began in 2012 in the Arabian peninsula with multiple outbreaks related to it in various parts of the globe. Various studies have suggested how these viruses made their entry from their natural reservoir bats via intermediate host like civets and camels in case of SARS-CoV and MERS-CoV respectively. The intermediate host of the SARS-CoV-2 still needs to be established. The SARS-CoV-2 has 96.2% similarity to the bat Severe Acute Respiratory Syndrome related-Coronavirus (SARSr-CoV RaTG13). SARS-CoV-2 has been found to be more distant in relation to SARS-CoV (79%) and MERS-CoV (50%). At the whole genome sequence level pangolin CoV and SARSr-CoV RaTG13 show 91.02% and 96.2% similarity with SARS-CoV-2 but the S1 subunit of spike protein of pangolin CoV is more closely related to SARS-CoV-2 than SARSr-CoV RaTG13. The genetic analysis of the currently circulating strains of the pandemic have shown 99.98-100% similarity in their genomes implying a recent shift to humans. The animal source of SARS-CoV-2 needs to be identified to implement control measures in the present pandemic. Also, how the virus moves interspecies will help predict and prevent future pandemics.
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Affiliation(s)
- K.B. Anand
- Associate Professor, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - S. Karade
- Assistant Professor, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - S. Sen
- Professor & Head, Department of Microbiology, Armed Forces Medical College, Pune 411040, India
| | - R.M. Gupta
- Professor (Microbiology) & Dean and Deputy Commandant, Armed Forces Medical College, Pune 411040, India
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Emergence and Selection of a Highly Pathogenic Avian Influenza H7N3 Virus. J Virol 2020; 94:JVI.01818-19. [PMID: 31969434 DOI: 10.1128/jvi.01818-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 01/09/2020] [Indexed: 01/21/2023] Open
Abstract
Low-pathogenicity avian influenza (LPAI) viruses of subtypes H5 and H7 have the ability to spontaneously mutate to highly pathogenic (HPAI) virus variants, causing high mortality in poultry. The highly pathogenic phenotype is caused by mutation of the hemagglutinin (HA) cleavage site, but additional mutations may play a role. Evidence from the field for the switch to high pathogenicity remains scarce. This study provides direct evidence for LPAI-to-HPAI virus mutation during H7N3 infection of a turkey farm in the Netherlands. No severe clinical symptoms were reported at the farm, but deep sequencing of isolates from the infected turkeys revealed a minority of HPAI virus sequences (0.06%) in the virus population. The HPAI virus contained a 12-nucleotide insertion in the HA cleavage site that was likely introduced by a single event as no intermediates with shorter inserts were identified. This suggests nonhomologous recombination as the mechanism of insertion. Analysis of different organs of the infected turkeys showed the largest amount of HPAI virus in the lung (4.4%). The HPAI virus was rapidly selected in experimentally infected chickens after both intravenous and intranasal/intratracheal inoculation with a mixed virus preparation. Full-genome sequencing revealed that both pathotypes contained a deletion in the stalk region of the neuraminidase protein. We identified additional mutations in HA and polymerase basic protein 1 (PB1) in the HPAI virus, which were already present as minority variants in the LPAI virus population. Our findings provide more insight into the molecular changes and mechanisms involved in the emergence and selection of HPAI viruses.IMPORTANCE Low-pathogenicity avian influenza (LPAI) viruses circulate in wild birds and can be transmitted to poultry. LPAI viruses can mutate to become highly pathogenic avian influenza (HPAI) viruses causing severe disease and death in poultry. Little is known about this switch to high pathogenicity. We isolated an LPAI H7N3 virus from an infected turkey farm and showed that this contains small amounts of HPAI virus. The HPAI virus rapidly outcompeted the LPAI virus in chickens that were experimentally infected with this mixture of viruses. We analyzed the genome sequences of the LPAI and HPAI viruses and identified several changes that may be important for a virus to become highly pathogenic. This knowledge may be used for timely identification of LPAI viruses that pose a risk of becoming highly pathogenic in the field.
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72
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Insertion of Basic Amino Acids in the Hemagglutinin Cleavage Site of H4N2 Avian Influenza Virus (AIV)-Reduced Virus Fitness in Chickens is Restored by Reassortment with Highly Pathogenic H5N1 AIV. Int J Mol Sci 2020; 21:ijms21072353. [PMID: 32231159 PMCID: PMC7178042 DOI: 10.3390/ijms21072353] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 02/02/2023] Open
Abstract
Highly pathogenic (HP) avian influenza viruses (AIVs) are naturally restricted to H5 and H7 subtypes with a polybasic cleavage site (CS) in hemagglutinin (HA) and any AIV with an intravenous pathogenicity index (IVPI) ≥ 1.2. Although only a few non-H5/H7 viruses fulfill the criteria of HPAIV; it remains unclear why these viruses did not spread in domestic birds. In 2012, a unique H4N2 virus with a polybasic CS 322PEKRRTR/G329 was isolated from quails in California which, however, was avirulent in chickens. This is the only known non-H5/H7 virus with four basic amino acids in the HACS. Here, we investigated the virulence of this virus in chickens after expansion of the polybasic CS by substitution of T327R (322PEKRRRR/G329) or T327K (322PEKRRKR/G329) with or without reassortment with HPAIV H5N1 and H7N7. The impact of single mutations or reassortment on virus fitness in vitro and in vivo was studied. Efficient cell culture replication of T327R/K carrying H4N2 viruses increased by treatment with trypsin, particularly in MDCK cells, and reassortment with HPAIV H5N1. Replication, virus excretion and bird-to-bird transmission of H4N2 was remarkably compromised by the CS mutations, but restored after reassortment with HPAIV H5N1, although not with HPAIV H7N7. Viruses carrying the H4-HA with or without R327 or K327 mutations and the other seven gene segments from HPAIV H5N1 exhibited high virulence and efficient transmission in chickens. Together, increasing the number of basic amino acids in the H4N2 HACS was detrimental for viral fitness particularly in vivo but compensated by reassortment with HPAIV H5N1. This may explain the absence of non-H5/H7 HPAIV in poultry.
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73
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Rehman SU, Shafique L, Ihsan A, Liu Q. Evolutionary Trajectory for the Emergence of Novel Coronavirus SARS-CoV-2. Pathogens 2020; 9:pathogens9030240. [PMID: 32210130 PMCID: PMC7157669 DOI: 10.3390/pathogens9030240] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/18/2020] [Accepted: 03/21/2020] [Indexed: 01/16/2023] Open
Abstract
Over the last two decades, the world experienced three outbreaks of coronaviruses with elevated morbidity rates. Currently, the global community is facing emerging virus SARS-CoV-2 belonging to Betacoronavirus, which appears to be more transmissible but less deadly than SARS-CoV. The current study aimed to track the evolutionary ancestors and different evolutionary strategies that were genetically adapted by SARS-CoV-2. Our whole-genome analysis revealed that SARS-CoV-2 was the descendant of Bat SARS/SARS-like CoVs and bats served as a natural reservoir. SARS-CoV-2 used mutations and recombination as crucial strategies in different genomic regions including the envelop, membrane, nucleocapsid, and spike glycoproteins to become a novel infectious agent. We confirmed that mutations in different genomic regions of SARS-CoV-2 have specific influence on virus reproductive adaptability, allowing for genotype adjustment and adaptations in rapidly changing environments. Moreover, for the first time we identified nine putative recombination patterns in SARS-CoV-2, which encompass spike glycoprotein, RdRp, helicase and ORF3a. Six recombination regions were spotted in the S gene and are undoubtedly important for evolutionary survival, meanwhile this permitted the virus to modify superficial antigenicity to find a way from immune reconnaissance in animals and adapt to a human host. With these combined natural selected strategies, SARS-CoV-2 emerged as a novel virus in human society.
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Affiliation(s)
- Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources of Guangxi University, Nanning 530005, China; (S.u.R.); (L.S.)
| | - Laiba Shafique
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources of Guangxi University, Nanning 530005, China; (S.u.R.); (L.S.)
| | - Awais Ihsan
- Department of Biosciences, COMSATS University Islamabad, Sahiwal Campus 57000, Pakistan
- College of Pharmacy, South Central University for Nationalities, Wuhan 430074, China
- Correspondence: (A.I.); (Q.L.); Tel.: +86-13878805296 (Q.L.)
| | - Qingyou Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources of Guangxi University, Nanning 530005, China; (S.u.R.); (L.S.)
- Correspondence: (A.I.); (Q.L.); Tel.: +86-13878805296 (Q.L.)
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74
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Yeo SJ, Than DD, Park HS, Sung HW, Park H. Molecular Characterization of a Novel Avian Influenza A (H2N9) Strain Isolated from Wild Duck in Korea in 2018. Viruses 2019; 11:v11111046. [PMID: 31717636 PMCID: PMC6893532 DOI: 10.3390/v11111046] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 11/02/2019] [Accepted: 11/06/2019] [Indexed: 01/03/2023] Open
Abstract
A novel avian influenza virus (A/wild duck/Korea/K102/2018) (H2N9) was isolated from wild birds in South Korea in 2018, and phylogenetic and molecular analyses were conducted on complete gene sequences obtained by next-generation sequencing. Phylogenetic analysis indicated that the hemagglutinin (HA) and neuraminidase (NA) genes of the A/wild duck/Korea/K102/2018 (H2N9) virus belonged to the Eurasian countries, whereas other internal genes (polymerase basic protein 1 (PB1), PB2, nucleoprotein (NP), polymerase acidic protein (PA), matrix protein (M), and non-structural protein (NS)) belonged to the East Asian countries. A monobasic amino acid (PQIEPR/GLF) at the HA cleavage site, E627 in the PB2 gene, and no deletion of the stalk region in the NA gene indicated that the A/wild duck/Korea/K102/2018 (H2N9) isolate was a typical low pathogenicity avian influenza (LPAI). Nucleotide sequence similarity analysis of HA revealed that the highest homology (98.34%) is to that of A/duck/Mongolia/482/2015 (H2N3), and amino acid sequence of NA was closely related to that of A/duck/Bangladesh/8987/2010 (H10N9) (96.45%). In contrast, internal genes showed homology higher than 98% compared to those of other isolates derived from duck and wild birds of China or Japan in 2016–2018. The newly isolated A/wild duck/Korea/K102/2018 (H2N9) strain is the first reported avian influenza virus in Korea, and may have evolved from multiple genotypes in wild birds and ducks in Mongolia, China, and Japan.
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Affiliation(s)
- Seon-Ju Yeo
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
| | - Duc-Duong Than
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
| | - Hong-Seog Park
- GnCBio Inc, 4F, Yegan Plaza, 36, Banseok-ro, Yuseong-gu, Daejeon 34069, Korea;
| | - Haan Woo Sung
- College of Veterinary Medicine, Kangwon National University, Chuncheon 24341, Korea
- Correspondence: (H.W.S.); (H.P.)
| | - Hyun Park
- Zoonosis Research Center, Department of Infection Biology, School of Medicine, Wonkwang University, Iksan 54538, Korea; (S.-J.Y.); (D.-D.T.)
- Correspondence: (H.W.S.); (H.P.)
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75
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Gultyaev AP, Richard M, Spronken MI, Olsthoorn RCL, Fouchier RAM. Conserved structural RNA domains in regions coding for cleavage site motifs in hemagglutinin genes of influenza viruses. Virus Evol 2019; 5:vez034. [PMID: 31456885 PMCID: PMC6704317 DOI: 10.1093/ve/vez034] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The acquisition of a multibasic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein is the main determinant of the conversion of low pathogenic avian influenza viruses into highly pathogenic strains, facilitating HA cleavage and virus replication in a broader range of host cells. In nature, substitutions or insertions in HA RNA genomic segments that code for multiple basic amino acids have been observed only in the HA genes of two out of sixteen subtypes circulating in birds, H5 and H7. Given the compatibility of MBCS motifs with HA proteins of numerous subtypes, this selectivity was hypothesized to be determined by the existence of specific motifs in HA RNA, in particular structured domains. In H5 and H7 HA RNAs, predictions of such domains have yielded alternative conserved stem-loop structures with the cleavage site codons in the hairpin loops. Here, potential RNA secondary structures were analyzed in the cleavage site regions of HA segments of influenza viruses of different types and subtypes. H5- and H7-like stem-loop structures were found in all known influenza A virus subtypes and in influenza B and C viruses with homology modeling. Nucleotide covariations supported this conservation to be determined by RNA structural constraints that are stronger in the domain-closing bottom stems as compared to apical parts. The structured character of this region in (sub-)types other than H5 and H7 indicates its functional importance beyond the ability to evolve toward an MBCS responsible for a highly pathogenic phenotype.
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Affiliation(s)
- Alexander P Gultyaev
- Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.,Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - Monique I Spronken
- Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
| | - René C L Olsthoorn
- Leiden Institute of Chemistry, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands
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76
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A viral race for primacy: co-infection of a natural pair of low and highly pathogenic H7N7 avian influenza viruses in chickens and embryonated chicken eggs. Emerg Microbes Infect 2018; 7:204. [PMID: 30514922 PMCID: PMC6279742 DOI: 10.1038/s41426-018-0204-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/14/2018] [Accepted: 11/17/2018] [Indexed: 11/10/2022]
Abstract
Highly pathogenic avian influenza virus (HPAIV) infection in poultry caused devastating mortality and economic losses. HPAIV of subtypes H5 and H7 emerge from precursor viruses of low pathogenicity (LP) by spontaneous mutation associated with a shift in the susceptibility of the endoproteolytic cleavage site of the viral hemagglutinin protein from trypsin- to furin-like proteases. A recently described natural pair of LP/HP H7N7 viruses derived from two spatio-temporally linked outbreaks in layer chickens was used to study how a minority of mutated HP virions after de novo generation in a single host might gain primacy. Co-infection experiments in embryonated eggs and in chickens were conducted to investigate amplification, spread and transmissionof HPAIV within a poultry population that experiences concurrent infection by an antigenically identical LP precursor virus. Simultaneous LPAIV co-infection (inoculum dose of 106 egg-infectious dose 50% endpoint (EID50)/0.5 mL) withincreasing titers of HPAIV from 101 to 105.7 EID50/0.5 mL) had a significant impeding impact on HP H7 replication, viral excretion kinetics, clinical signs and histopathological lesions (in vivo) and on embryo mortality (in ovo). LP/HP co-infected chickens required a hundredfold higher virus dose (HPAIV inoculum of 105 EID50) compared to HPAIV mono-infection (HPAIV inoculum of 103 EID50) to develop overt clinical signs, mortality and virus spread to uninfected sentinels. Escape and spread of HP phenotypes after de novo generation in an index host may therefore be highly precarious due to significant competition with co-circulating LP precursor virus.
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77
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Delgadillo-Gutiérrez K, Ribas-Aparicio RM, Jiménez-Alberto A, Aparicio-Ozores G, Castelán-Vega JA. Stability of retroviral pseudotypes carrying the hemagglutinin of avian influenza viruses under various storage conditions. J Virol Methods 2018; 263:44-49. [PMID: 30347199 DOI: 10.1016/j.jviromet.2018.10.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 09/09/2018] [Accepted: 10/16/2018] [Indexed: 11/25/2022]
Abstract
Retroviral pseudotypes are broadly used as safe instruments to mimic the structure and surface of highly pathogenic viruses. They have been employed for the discovery of new drugs, as diagnostic tools in vaccine studies, and part of serological assays. Because of their widespread use in research and their potential as tools for quality control, it is important to know their shelf life, stability, and best storage conditions. In this study, we produced pseudotypes carrying the lacZ reporter gene and the hemagglutinin (HA) of avian influenza virus subtypes H5 and H7 to investigate their stability under various storage conditions. We produced pseudotypes with titers of approximately 106 RLU/mL, which decreased to 105-106 RLU/mL after short-term storage at 4 °C (up to 4 weeks). Stability was maintained after long-term storage at -20 °C (up to 12 months), even under storage variations such as freeze-thaw cycles. We conclude that, although the titers decreased by 1 log10 under the different storage conditions, the remaining titers can be readily applicable in many techniques, such as neutralization assays. These findings show that large quantities of retroviral pseudotypes can be safely stored for short- or long-term use, allowing standardization and reduced variation in assays involving retroviral pseudotypes.
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Affiliation(s)
- Karen Delgadillo-Gutiérrez
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Rosa María Ribas-Aparicio
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Alicia Jiménez-Alberto
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico
| | - Juan A Castelán-Vega
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional (IPN), Mexico City, Mexico.
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78
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Evolution of high pathogenicity of H5 avian influenza virus: haemagglutinin cleavage site selection of reverse-genetics mutants during passage in chickens. Sci Rep 2018; 8:11518. [PMID: 30068964 PMCID: PMC6070550 DOI: 10.1038/s41598-018-29944-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/18/2018] [Indexed: 01/31/2023] Open
Abstract
Low pathogenicity avian influenza viruses (LPAIVs) are generally asymptomatic in their natural avian hosts. LPAIVs can evolve into highly pathogenic forms, which can affect avian and human populations with devastating consequences. The switch to highly pathogenic avian influenza virus (HPAIV) from LPAIV precursors requires the acquisition of multiple basic amino acids in the haemagglutinin cleavage site (HACS) motif. Through reverse genetics of an H5N1 HPAIV, and experimental infection of chickens, we determined that viruses containing five or more basic amino acids in the HACS motif were preferentially selected over those with three to four basic amino acids, leading to rapid replacement with virus types containing extended HACS motifs. Conversely, viruses harbouring low pathogenicity motifs containing two basic amino acids did not readily evolve to extended forms, suggesting that a single insertion of a basic amino acid into the cleavage site motif of low-pathogenic viruses may lead to escalating selection for extended motifs. Our results may explain why mid-length forms are rarely detected in nature. The stability of the short motif suggests that pathogenicity switching may require specific conditions of intense selection pressure (such as with high host density) to boost selection of the initial mid-length HACS forms.
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79
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Seekings AH, Slomka MJ, Russell C, Howard WA, Choudhury B, Nuñéz A, Löndt BZ, Cox W, Ceeraz V, Thorén P, Irvine RM, Manvell RJ, Banks J, Brown IH. Direct evidence of H7N7 avian influenza virus mutation from low to high virulence on a single poultry premises during an outbreak in free range chickens in the UK, 2008. INFECTION GENETICS AND EVOLUTION 2018; 64:13-31. [PMID: 29883773 DOI: 10.1016/j.meegid.2018.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 05/24/2018] [Accepted: 06/03/2018] [Indexed: 11/30/2022]
Abstract
H5 and H7 subtypes of low pathogenicity avian influenza viruses (LPAIVs) have the potential to evolve into highly pathogenic avian influenza viruses (HPAIVs), causing high mortality in galliforme poultry with substantial economic losses for the poultry industry. This study provides direct evidence of H7N7 LPAIV mutation to HPAIV on a single poultry premises during an outbreak that occurred in June 2008 in free range laying hens in Oxfordshire, UK. We report the first detection of a rare di-basic cleavage site (CS) motif (PEIPKKRGLF), unique to galliformes, that has previously been associated with a LPAIV phenotype. Three distinct HPAIV CS sequences (PEIPKRKKRGLF, PEIPKKKKRGLF and PEIPKKKKKKRGLF) were identified in the infected sheds suggesting molecular evolution at the outbreak premises. Further evidence for H7N7 LPAIV preceding mutation to HPAIV was derived by examining clinical signs, epidemiological descriptions and analysing laboratory results on the timing and proportions of seroconversion and virus shedding at each infected shed on the premises. In addition to describing how the outbreak was diagnosed and managed via statutory laboratory testing, phylogenetic analysis revealed reassortant events during 2006-2008 that suggested likely incursion of a wild bird origin LPAIV precursor to the H7N7 HPAIV outbreak. Identifying a precursor LPAIV is important for understanding the molecular changes and mechanisms involved in the emergence of HPAIV. This information can lead to understanding how and why only some H7 LPAIVs appear to readily mutate to HPAIV.
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Affiliation(s)
- A H Seekings
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom.
| | - M J Slomka
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - C Russell
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - W A Howard
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - B Choudhury
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - A Nuñéz
- Pathology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - B Z Löndt
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - W Cox
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - V Ceeraz
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - P Thorén
- Swedish Agricultural University (SLU), Uppsala, Sweden
| | - R M Irvine
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - R J Manvell
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - J Banks
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
| | - I H Brown
- Virology Department, Animal and Plant Health Agency (APHA-Weybridge), Addlestone, Surrey KT15 3NB, United Kingdom
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80
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Dietze K, Graaf A, Homeier-Bachmann T, Grund C, Forth L, Pohlmann A, Jeske C, Wintermann M, Beer M, Conraths FJ, Harder T. From low to high pathogenicity-Characterization of H7N7 avian influenza viruses in two epidemiologically linked outbreaks. Transbound Emerg Dis 2018; 65:1576-1587. [PMID: 29790657 DOI: 10.1111/tbed.12906] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 04/09/2018] [Accepted: 04/13/2018] [Indexed: 01/05/2023]
Abstract
The ability of low pathogenic (LP) avian influenza viruses (AIV) of the subtypes H5 and H7 to mutate spontaneously to highly pathogenic (HP) variants is the main reason for their stringent control. On-the-spot evidence from the field of mutations in LPAIV to render the virus into nascent HP variants is scarce. Epidemiological investigations and molecular characterization of two spatiotemporally linked outbreaks caused by LP, and subsequently, HPAIV H7N7 in two-layer farms in Germany yielded such evidence. The outbreaks occurred within 45 days on farms 400 m apart. The LP progenitor virus was identified on both farms, with its putative HP inheritor cocirculating and then dominating on the second farm. As postulated before, mutations in the hemagglutinin cleavage site (HACS) proved to be the most decisive change in the genome of HPAIV, in this case, it was mutated from monobasic (LP) PEIPKGR*GLF into polybasic (HP) PEIPKRKRR*GLF. The full-length genome sequences of both viruses were nearly identical with only ten coding mutations outside the HACS scattered along six genome segments in the HPAIV. Five of these were already present as minor variants in the LPAIV quasispecies of the LPAI-only affected farm. H7-specific seroconversion of part of the chicken population together with the codetection of LPAIV HACS sequences in swab samples of the HPAI outbreak farm suggested an initial introduction of the LP progenitor and a subsequent switch to HPAIV H7N7 after the incursion. The findings provide rare field evidence for a shift in pathogenicity of a notifiable AIV infection and re-inforce the validity of current approaches of control measures to curtail low pathogenic H5 and H7 virus circulation in poultry.
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Affiliation(s)
- Klaas Dietze
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | - Annika Graaf
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | | | - Leonie Forth
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | - Christa Jeske
- Niedersächsisches Landesamt für Verbraucherschutz und Lebensmittelsicherheit (LAVES), Wardenburg, Germany
| | | | - Martin Beer
- Friedrich-Loeffler-Institut, Greifswald, Germany
| | | | - Timm Harder
- Friedrich-Loeffler-Institut, Greifswald, Germany
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81
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Three amino acid substitutions in the NS1 protein change the virus replication of H5N1 influenza virus in human cells. Virology 2018; 519:64-73. [PMID: 29677653 DOI: 10.1016/j.virol.2018.04.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 04/05/2018] [Accepted: 04/10/2018] [Indexed: 12/15/2022]
Abstract
Influenza A viruses have sophisticated strategies to promote their own replication. Here, we found that three H5N1 influenza viruses display different replication patterns in human A549 and macrophage cells. The HN01 virus displayed poor replication compared to HN021 and JS01. In addition, the HN01 virus was unable to counteract the interferon response and block general gene expression. This capability was restored by three amino acid substitutions on the NS1 protein: K55E, K66E, and C133F, resulting in recovered binding to CPSF30 and decreased interferon response activity. Furthermore, a recombinant HN01 virus expressing either NS1-C133F or the triple mutation replicate with higher titers in human A549 cells and macrophages compared to the parent virus. These three amino acid mutations reveal a new pathway to alter H5N1 virus replication.
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82
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Zhang K, Xu WW, Zhang Z, Liu J, Li J, Sun L, Sun W, Jiao P, Sang X, Ren Z, Yu Z, Li Y, Feng N, Wang T, Wang H, Yang S, Zhao Y, Zhang X, Wilker PR, Liu W, Liao M, Chen H, Gao Y, Xia X. The innate immunity of guinea pigs against highly pathogenic avian influenza virus infection. Oncotarget 2018; 8:30422-30437. [PMID: 28418930 PMCID: PMC5444753 DOI: 10.18632/oncotarget.16503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/27/2017] [Indexed: 12/20/2022] Open
Abstract
H5N1 avian influenza viruses are a major pandemic concern. In contrast to the highly virulent phenotype of H5N1 in humans and many animal models, guinea pigs do not typically display signs of severe disease in response to H5N1 virus infection. Here, proteomic and transcriptional profiling were applied to identify host factors that account for the observed attenuation of A/Tiger/Harbin/01/2002 (H5N1) virulence in guinea pigs. RIG-I and numerous interferon stimulated genes were among host proteins with altered expression in guinea pig lungs during H5N1 infection. Overexpression of RIG-I or the RIG-I adaptor protein MAVS in guinea pig cell lines inhibited H5N1 replication. Endogenous GBP-1 expression was required for RIG-I mediated inhibition of viral replication upstream of the activity of MAVS. Furthermore, we show that guinea pig complement is involved in viral clearance, the regulation of inflammation, and cellular apoptosis during influenza virus infection of guinea pigs. This work uncovers features of the guinea pig innate immune response to influenza that may render guinea pigs resistant to highly pathogenic influenza viruses.
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Affiliation(s)
- Kun Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China.,Philips Institute for Oral Health Research, School of Dentistry, Virginia Commonwealth University, Richmond, Virginia, 23298, USA
| | - Wei Wei Xu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhaowei Zhang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Jing Liu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Jing Li
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Lijuan Sun
- Department of Influenza Vaccine, Changchun Institute of Biological Product, Changchun, 130062, PR China
| | - Weiyang Sun
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Peirong Jiao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Xiaoyu Sang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhiguang Ren
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Zhijun Yu
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Yuanguo Li
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Na Feng
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Tiecheng Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Hualei Wang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Songtao Yang
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Yongkun Zhao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Xuemei Zhang
- Department of Influenza Vaccine, Changchun Institute of Biological Product, Changchun, 130062, PR China
| | - Peter R Wilker
- Department of Microbiology, University of Wisconsin La Crosse, La Crosse, Wisconsin, 54601, USA
| | - WenJun Liu
- CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Ming Liao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, 510642, PR China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, PR China
| | - Yuwei Gao
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
| | - Xianzhu Xia
- Key Laboratory of Jilin Province for Zoonosis Prevention and Control, The Military Veterinary Institute, Academy of Military Medical Science of PLA, Changchun, 130122, PR China
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83
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Ogawa H, Kajihara M, Nao N, Shigeno A, Fujikura D, Hang'ombe BM, Mweene AS, Mutemwa A, Squarre D, Yamada M, Higashi H, Sawa H, Takada A. Characterization of a Novel Bat Adenovirus Isolated from Straw-Colored Fruit Bat (Eidolon helvum). Viruses 2017; 9:v9120371. [PMID: 29207524 PMCID: PMC5744146 DOI: 10.3390/v9120371] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 11/27/2017] [Accepted: 11/30/2017] [Indexed: 12/13/2022] Open
Abstract
Bats are important reservoirs for emerging zoonotic viruses. For extensive surveys of potential pathogens in straw-colored fruit bats (Eidolon helvum) in Zambia, a total of 107 spleen samples of E. helvum in 2006 were inoculated onto Vero E6 cells. The cell culture inoculated with one of the samples (ZFB06-106) exhibited remarkable cytopathic changes. Based on the ultrastructural property in negative staining and cross-reactivity in immunofluorescence assays, the virus was suspected to be an adenovirus, and tentatively named E. helvum adenovirus 06-106 (EhAdV 06-106). Analysis of the full-length genome of 30,134 bp, determined by next-generation sequencing, showed the presence of 28 open reading frames. Phylogenetic analyses confirmed that EhAdV 06-106 represented a novel bat adenovirus species in the genus Mastadenovirus. The virus shared similar characteristics of low G + C contents with recently isolated members of species Bat mastadenoviruses E, F and G, from which EhAdV 06-106 diverged by more than 15% based on the distance matrix analysis of DNA polymerase amino acid sequences. According to the taxonomic criteria, we propose the tentative new species name “Bat mastadenovirus H”. Because EhAdV 06-106 exhibited a wide in vitro cell tropism, the virus might have a potential risk as an emerging virus through cross-species transmission.
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Affiliation(s)
- Hirohito Ogawa
- Department of Virology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
| | - Naganori Nao
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
| | - Asako Shigeno
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
| | - Daisuke Fujikura
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
| | - Bernard M Hang'ombe
- Department of Paraclinical Studies, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
| | - Aaron S Mweene
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
| | - Alisheke Mutemwa
- Provincial Veterinary Office, Department of Veterinary Services, Ministry of Fisheries and Livestock, P.O. Box 70416, Ndola 50100, Zambia.
| | - David Squarre
- Department of National Parks and Wildlife, Ministry of Tourism and Arts, Private Bag 1, Chilanga 10101, Zambia.
| | - Masao Yamada
- Department of Virology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558, Japan.
| | - Hideaki Higashi
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
- Division of Infection and Immunity, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
- Hokudai Center for Zoonosis Control in Zambia, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
| | - Hirofumi Sawa
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
- Global Virus Network, 801 W Baltimore St, Baltimore, MD 21201, USA.
| | - Ayato Takada
- Department of Disease Control, School of Veterinary Medicine, University of Zambia, P.O. Box 32379, Lusaka 10101, Zambia.
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
- Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, N20, W10, Kita-ku, Sapporo 001-0020, Japan.
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More S, Bicout D, Bøtner A, Butterworth A, Calistri P, Depner K, Edwards S, Garin-Bastuji B, Good M, Gortázar Schmidt C, Michel V, Miranda MA, Nielsen SS, Raj M, Sihvonen L, Spoolder H, Thulke HH, Velarde A, Willeberg P, Winckler C, Breed A, Brouwer A, Guillemain M, Harder T, Monne I, Roberts H, Baldinelli F, Barrucci F, Fabris C, Martino L, Mosbach-Schulz O, Verdonck F, Morgado J, Stegeman JA. Avian influenza. EFSA J 2017; 15:e04991. [PMID: 32625288 PMCID: PMC7009867 DOI: 10.2903/j.efsa.2017.4991] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Previous introductions of highly pathogenic avian influenza virus (HPAIV) to the EU were most likely via migratory wild birds. A mathematical model has been developed which indicated that virus amplification and spread may take place when wild bird populations of sufficient size within EU become infected. Low pathogenic avian influenza virus (LPAIV) may reach similar maximum prevalence levels in wild bird populations to HPAIV but the risk of LPAIV infection of a poultry holding was estimated to be lower than that of HPAIV. Only few non-wild bird pathways were identified having a non-negligible risk of AI introduction. The transmission rate between animals within a flock is assessed to be higher for HPAIV than LPAIV. In very few cases, it could be proven that HPAI outbreaks were caused by intrinsic mutation of LPAIV to HPAIV but current knowledge does not allow a prediction as to if, and when this could occur. In gallinaceous poultry, passive surveillance through notification of suspicious clinical signs/mortality was identified as the most effective method for early detection of HPAI outbreaks. For effective surveillance in anseriform poultry, passive surveillance through notification of suspicious clinical signs/mortality needs to be accompanied by serological surveillance and/or a virological surveillance programme of birds found dead (bucket sampling). Serosurveillance is unfit for early warning of LPAI outbreaks at the individual holding level but could be effective in tracing clusters of LPAIV-infected holdings. In wild birds, passive surveillance is an appropriate method for HPAIV surveillance if the HPAIV infections are associated with mortality whereas active wild bird surveillance has a very low efficiency for detecting HPAIV. Experts estimated and emphasised the effect of implementing specific biosecurity measures on reducing the probability of AIV entering into a poultry holding. Human diligence is pivotal to select, implement and maintain specific, effective biosecurity measures.
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85
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Zhu W, Wang C, Wang BZ. From Variation of Influenza Viral Proteins to Vaccine Development. Int J Mol Sci 2017; 18:ijms18071554. [PMID: 28718801 PMCID: PMC5536042 DOI: 10.3390/ijms18071554] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Revised: 07/10/2017] [Accepted: 07/14/2017] [Indexed: 11/19/2022] Open
Abstract
Recurrent influenza epidemics and occasional pandemics are one of the most important global public health concerns and are major causes of human morbidity and mortality. Influenza viruses can evolve through antigen drift and shift to overcome the barriers of human immunity, leading to host adaption and transmission. Mechanisms underlying this viral evolution are gradually being elucidated. Vaccination is an effective method for the prevention of influenza virus infection. However, the emergence of novel viruses, including the 2009 pandemic influenza A (H1N1), the avian influenza A virus (H7N9), and the highly pathogenic avian influenza A virus (HPAI H5N1), that have infected human populations frequently in recent years reveals the tremendous challenges to the current influenza vaccine strategy. A better vaccine that provides protection against a wide spectrum of various influenza viruses and long-lasting immunity is urgently required. Here, we review the evolutionary changes of several important influenza proteins and the influence of these changes on viral antigenicity, host adaption, and viral pathogenicity. Furthermore, we discuss the development of a potent universal influenza vaccine based on this knowledge.
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Affiliation(s)
- Wandi Zhu
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
| | - Chao Wang
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
| | - Bao-Zhong Wang
- Center for Inflammation, Immunity & Infection, Georgia State University Institute for Biomedical Sciences, Atlanta, GA 30303, USA.
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