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Yamanaka A, Rattanaamnuaychai P, Matsuda M, Suzuki R, Matsuura Y, Tatsumi M, Konishi E. Engineered flavivirus vaccines control induction of crossreactive infection-enhancing and -neutralizing antibodies. Vaccine 2022; 40:6004-6011. [PMID: 36109279 DOI: 10.1016/j.vaccine.2022.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/20/2022] [Accepted: 09/03/2022] [Indexed: 11/16/2022]
Abstract
Flaviviruses are important human pathogens because of their global distribution and disease severity. The high structural similarity among flaviviruses induces cross-immunity, with individual flaviviruses exhibiting crossreactive infection-enhancing and/or -neutralizing activities against other flaviviruses. Unlike neutralizing antibodies, enhancing antibodies may increase the risk of disease severity. Vaccine-induced enhancement remains a concern in the development of flavivirus vaccines. Here, we immunized mice with DNA vaccine candidates (pcJEME, pcWNME or pcZIKME) against Japanese encephalitis virus (JEV), West Nile virus (WNV) or Zika virus (ZIKV), respectively, and investigated crossreactive neutralizing and enhancing antibody activities against seven flaviviruses. pcZIKME induced higher cross-neutralization against dengue viruses than against JEV and WNV. Moreover, pcZIKME with a single amino acid substitution (D87N) showed an increase in crossreactive neutralizing activity and a decrease in enhancing activities against other flaviviruses. A similar trend was observed in pcWNME. Engineered antigen might contribute to the development of safe and effective flavivirus vaccines.
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Affiliation(s)
- Atsushi Yamanaka
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand; Mahidol-Osaka Center for Infectious Diseases, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
| | - Pimploy Rattanaamnuaychai
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Mami Matsuda
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Ryosuke Suzuki
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshiharu Matsuura
- Laboratory of Virus Control, Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan; Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masashi Tatsumi
- Thailand-Japan Research Collaboration Center on Emerging and Re-emerging Infections (RCC-ERI), Department of Medical Sciences, Ministry of Public Health, Nonthaburi, Thailand
| | - Eiji Konishi
- BIKEN Endowed Department of Dengue Vaccine Development, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
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Jacob Machado D, Scott R, Guirales S, Janies DA. Fundamental evolution of all Orthocoronavirinae including three deadly lineages descendent from Chiroptera-hosted coronaviruses: SARS-CoV, MERS-CoV and SARS-CoV-2. Cladistics 2021; 37:461-488. [PMID: 34570933 PMCID: PMC8239696 DOI: 10.1111/cla.12454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2021] [Indexed: 12/14/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in humans in 2002. Despite reports showing Chiroptera as the original animal reservoir of SARS-CoV, many argue that Carnivora-hosted viruses are the most likely origin. The emergence of the Middle East respiratory syndrome coronavirus (MERS-CoV) in 2012 also involves Chiroptera-hosted lineages. However, factors such as the lack of comprehensive phylogenies hamper our understanding of host shifts once MERS-CoV emerged in humans and Artiodactyla. Since 2019, the origin of SARS-CoV-2, causative agent of coronavirus disease 2019 (COVID-19), added to this episodic history of zoonotic transmission events. Here we introduce a phylogenetic analysis of 2006 unique and complete genomes of different lineages of Orthocoronavirinae. We used gene annotations to align orthologous sequences for total evidence analysis under the parsimony optimality criterion. Deltacoronavirus and Gammacoronavirus were set as outgroups to understand spillovers of Alphacoronavirus and Betacoronavirus among ten orders of animals. We corroborated that Chiroptera-hosted viruses are the sister group of SARS-CoV, SARS-CoV-2 and MERS-related viruses. Other zoonotic events were qualified and quantified to provide a comprehensive picture of the risk of coronavirus emergence among humans. Finally, we used a 250 SARS-CoV-2 genomes dataset to elucidate the phylogenetic relationship between SARS-CoV-2 and Chiroptera-hosted coronaviruses.
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Affiliation(s)
- Denis Jacob Machado
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Rachel Scott
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Sayal Guirales
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
| | - Daniel A. Janies
- Department of Bioinformatics and GenomicsUniversity of North Carolina at Charlotte9331 Robert D. Snyder RdCharlotteNC28223USA
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3
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de Bernardi Schneider A, Osiowy C, Hostager R, Krarup H, Børresen M, Tanaka Y, Morriseau T, Wertheim JO. Analysis of Hepatitis B Virus Genotype D in Greenland Suggests the Presence of a Novel Quasi-Subgenotype. Front Microbiol 2021; 11:602296. [PMID: 33519744 PMCID: PMC7843931 DOI: 10.3389/fmicb.2020.602296] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/14/2020] [Indexed: 12/12/2022] Open
Abstract
A disproportionate number of Greenland's Inuit population are chronically infected with Hepatitis B virus (HBV; 5-10%). HBV genotypes B and D are most prevalent in the circumpolar Arctic. Here, we report 39 novel HBV/D sequences from individuals residing in southwestern Greenland. We performed phylodynamic analyses with ancient HBV DNA calibrators to investigate the origin and relationship of these taxa to other HBV sequences. We inferred a substitution rate of 1.4 × 10-5 [95% HPD 8.8 × 10-6, 2.0 × 10-5] and a time to the most recent common ancestor of 629 CE [95% HPD 37-1138 CE]. The Greenland taxa form a sister clade to HBV/D2 sequences, specifically New Caledonian and Indigenous Taiwanese sequences. The Greenland sequences share amino acid signatures with subgenotypes D1 and D2 and ~97% sequence identity. Our results suggest the classification of these novel sequences does not fit within the current nomenclature. Thus, we propose these taxa be considered a novel quasi-subgenotype.
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Affiliation(s)
| | - Carla Osiowy
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Reilly Hostager
- Department of Medicine, University of California San Diego, San Diego, CA, United States
| | - Henrik Krarup
- Department of Molecular Diagnostics, Aalborg University Hospital, Aalborg, Denmark
- Department of Medical Gastroenterology, Aalborg University Hospital, Aalborg, Denmark
- Clinical Institute, Aalborg University, Aalborg, Denmark
| | - Malene Børresen
- Department of Epidemiological Research, Statens Serum Institut, Copenhagen, Denmark
| | - Yasuhito Tanaka
- Department of Virology & Liver, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Taylor Morriseau
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Joel O. Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, United States
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Jacob Machado D, White RA, Kofsky J, Janies DA. Fundamentals of genomic epidemiology, lessons learned from the coronavirus disease 2019 (COVID-19) pandemic, and new directions. ANTIMICROBIAL STEWARDSHIP & HEALTHCARE EPIDEMIOLOGY : ASHE 2021; 1:e60. [PMID: 36168505 PMCID: PMC9495640 DOI: 10.1017/ash.2021.222] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 04/19/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic was one of the significant causes of death worldwide in 2020. The disease is caused by severe acute coronavirus syndrome (SARS) coronavirus 2 (SARS-CoV-2), an RNA virus of the subfamily Orthocoronavirinae related to 2 other clinically relevant coronaviruses, SARS-CoV and MERS-CoV. Like other coronaviruses and several other viruses, SARS-CoV-2 originated in bats. However, unlike other coronaviruses, SARS-CoV-2 resulted in a devastating pandemic. The SARS-CoV-2 pandemic rages on due to viral evolution that leads to more transmissible and immune evasive variants. Technology such as genomic sequencing has driven the shift from syndromic to molecular epidemiology and promises better understanding of variants. The COVID-19 pandemic has exposed critical impediments that must be addressed to develop the science of pandemics. Much of the progress is being applied in the developed world. However, barriers to the use of molecular epidemiology in low- and middle-income countries (LMICs) remain, including lack of logistics for equipment and reagents and lack of training in analysis. We review the molecular epidemiology literature to understand its origins from the SARS epidemic (2002-2003) through influenza events and the current COVID-19 pandemic. We advocate for improved genomic surveillance of SARS-CoV and understanding the pathogen diversity in potential zoonotic hosts. This work will require training in phylogenetic and high-performance computing to improve analyses of the origin and spread of pathogens. The overarching goals are to understand and abate zoonosis risk through interdisciplinary collaboration and lowering logistical barriers.
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Affiliation(s)
- Denis Jacob Machado
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- Author for correspondence: Denis Jacob Machado, PhD, Department of Bioinformatics and Genomics, College of Computing and Informatics, University of North Carolina at Charlotte, 9331 Robert D. Snyder Rd, BINF 224, Charlotte, NC28223. E-mail:
| | - Richard Allen White
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
- University of North Carolina at Charlotte, North Carolina Research Campus (NCRC), Kannapolis, North Carolina
| | - Janice Kofsky
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
| | - Daniel A. Janies
- University of North Carolina at Charlotte, College of Computing and Informatics, Department of Bioinformatics and Genomics, Charlotte, North Carolina
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Scroggs SLP, Andrade CC, Chinnasamy R, Azar SR, Schirtzinger EE, Garcia EI, Arterburn JB, Hanley KA, Rossi SL. Old Drugs with New Tricks: Efficacy of Fluoroquinolones to Suppress Replication of Flaviviruses. Viruses 2020; 12:v12091022. [PMID: 32933138 PMCID: PMC7551155 DOI: 10.3390/v12091022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 02/06/2023] Open
Abstract
Repurposing FDA-approved compounds could provide the fastest route to alleviate the burden of disease caused by flaviviruses. In this study, three fluoroquinolones, enoxacin, difloxacin and ciprofloxacin, curtailed replication of flaviviruses Zika (ZIKV), dengue (DENV), Langat (LGTV) and Modoc (MODV) in HEK-293 cells at low micromolar concentrations. Time-of-addition assays suggested that enoxacin suppressed ZIKV replication at an intermediate step in the virus life cycle, whereas ciprofloxacin and difloxacin had a wider window of efficacy. A129 mice infected with 1 × 105 plaque-forming units (pfu) ZIKV FSS13025 (n = 20) or phosphate buffered saline (PBS) (n = 11) on day 0 and treated with enoxacin at 10 mg/kg or 15 mg/kg or diluent orally twice daily on days 1–5 did not differ in weight change or virus titer in serum or brain. However, mice treated with enoxacin showed a significant, five-fold decrease in ZIKV titer in testes relative to controls. Mice infected with 1 × 102 pfu ZIKV (n = 13) or PBS (n = 13) on day 0 and treated with 15 mg/kg oral enoxacin or diluent twice daily pre-treatment and days 1–5 post-treatment also did not differ in weight and viral load in the serum, brain, and liver, but mice treated with enoxacin showed a significant, 2.5-fold decrease in ZIKV titer in testes relative to controls. ZIKV can be sexually transmitted, so reduction of titer in the testes by enoxacin should be further investigated.
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Affiliation(s)
- Stacey L. P. Scroggs
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (C.C.A.); (E.E.S.); (E.I.G.); (K.A.H.)
- Biology of Vector-Borne Viruses Section, Laboratory of Virology, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
- Correspondence:
| | - Christy C. Andrade
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (C.C.A.); (E.E.S.); (E.I.G.); (K.A.H.)
- Department of Biology, Gonzaga University, Spokane, WA 99258, USA
| | - Ramesh Chinnasamy
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA; (R.C.); (J.B.A.)
| | - Sasha R. Azar
- Institute for Translational Sciences, The University of University of Texas Medical Branch, Galveston, TX 77555, USA;
| | - Erin E. Schirtzinger
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (C.C.A.); (E.E.S.); (E.I.G.); (K.A.H.)
- Arthropod-borne Animal Diseases Research Unit, United States Department of Agriculture, Agricultural Research Service, Manhattan, KS 66506, USA
| | - Erin I. Garcia
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (C.C.A.); (E.E.S.); (E.I.G.); (K.A.H.)
- Science News, Washington, DC 20036, USA
| | - Jeffrey B. Arterburn
- Department of Chemistry and Biochemistry, New Mexico State University, Las Cruces, NM 88003, USA; (R.C.); (J.B.A.)
| | - Kathryn A. Hanley
- Department of Biology, New Mexico State University, Las Cruces, NM 88003, USA; (C.C.A.); (E.E.S.); (E.I.G.); (K.A.H.)
| | - Shannan L. Rossi
- Department of Pathology, The University of Texas Medical Branch, Galveston, TX 77555, USA;
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