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Heidema S, Stoepker IV, Flaherty G, Angelo KM, Post RAJ, Miller C, Libman M, Hamer DH, van den Heuvel ER, Huits R. From GeoSentinel data to epidemiological insights: a multidisciplinary effort towards artificial intelligence-supported detection of infectious disease outbreaks. J Travel Med 2024; 31:taae013. [PMID: 38236181 DOI: 10.1093/jtm/taae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/11/2024] [Accepted: 01/13/2024] [Indexed: 01/19/2024]
Affiliation(s)
- Stan Heidema
- Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Ivo V Stoepker
- Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Gerard Flaherty
- School of Medicine, University of Galway, University Road, Galway, H91 TK33, Ireland
- School of Medicine, International Medical University, Bukit Jalil, 57000, Kuala Lumpur, Malaysia
| | - Kristina M Angelo
- Division of Global Migration and Health, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA
| | - Richard A J Post
- Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Charles Miller
- Division of Global Migration and Health, National Center for Emerging and Zoonotic Infectious Disease, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA
| | - Michael Libman
- J.D. MacLean Centre for Tropical Diseases, McGill University, Room E05.1830, 1001 Boulevard Décarie, Montréal, Québec H4A 3J1, Canada
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Crosstown 308, 801 Massachusetts Avenue, Boston, MA 02118, USA
- Section of Infectious Diseases, Department of Medicine, Boston University Chobanian & Avedisian School of Medicine, Crosstown 308, 801 Massachusetts Avenue, Boston, MA 02118, USA
- Center for Emerging Infectious Diseases Policy and Research, Boston University, 111 Cummington Mall, #104, Boston, MA 02215, USA
| | - Edwin R van den Heuvel
- Department of Mathematics and Computer Science, Eindhoven University of Technology, Eindhoven, The Netherlands
- Department of Preventive Medicine and Epidemiology, School of Medicine, Boston University, 72 East Concord Street, Floor L-5, Boston, MA 02218, USA
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, 37024, Via Don A Sempreboni 5, Negrar di Valpolicella, Verona, Italy
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2
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Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CBF, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. Nat Commun 2024; 15:3508. [PMID: 38664380 PMCID: PMC11045810 DOI: 10.1038/s41467-024-47774-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.
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Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, CT, USA.
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Lauren M Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA
| | - Robert T Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mallery I Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Joshua L Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Andrew Hagy
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, FL, USA
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, FL, USA
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, FL, USA
| | | | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA
| | - Jorge L Muñoz-Jordán
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gilberto A Santiago
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Melanie Spillane
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
- Bureau for Global Health, United States Agency for International Development, Arlington, VA, USA
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Robert Paulino-Ramírez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Sayira Mueses
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Armando Peguero
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Francesca F Norman
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, CIBER de Enfermedades Infecciosas, IRYCIS, Hospital Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan-Carlos Galán
- Microbiology Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, Section of Infectious Diseases, Boston University School of Medicine, Center for Emerging Infectious Disease Policy and Research, Boston University, and National Emerging Infectious Disease Laboratory, Boston, MA, USA
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, FL, USA.
| | - Scott F Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, FL, USA.
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
- Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
- Yale Institute for Global Health, Yale University, New Haven, CT, USA.
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA.
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3
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Taylor-Salmon E, Hill V, Paul LM, Koch RT, Breban MI, Chaguza C, Sodeinde A, Warren JL, Bunch S, Cano N, Cone M, Eysoldt S, Garcia A, Gilles N, Hagy A, Heberlein L, Jaber R, Kassens E, Colarusso P, Davis A, Baudin S, Rico E, Mejía-Echeverri Á, Scott B, Stanek D, Zimler R, Muñoz-Jordán JL, Santiago GA, Adams LE, Paz-Bailey G, Spillane M, Katebi V, Paulino-Ramírez R, Mueses S, Peguero A, Sánchez N, Norman FF, Galán JC, Huits R, Hamer DH, Vogels CB, Morrison A, Michael SF, Grubaugh ND. Travel surveillance uncovers dengue virus dynamics and introductions in the Caribbean. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.11.11.23298412. [PMID: 37986857 PMCID: PMC10659465 DOI: 10.1101/2023.11.11.23298412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Dengue is the most prevalent mosquito-borne viral disease in humans, and cases are continuing to rise globally. In particular, islands in the Caribbean have experienced more frequent outbreaks, and all four dengue virus (DENV) serotypes have been reported in the region, leading to hyperendemicity and increased rates of severe disease. However, there is significant variability regarding virus surveillance and reporting between islands, making it difficult to obtain an accurate understanding of the epidemiological patterns in the Caribbean. To investigate this, we used travel surveillance and genomic epidemiology to reconstruct outbreak dynamics, DENV serotype turnover, and patterns of spread within the region from 2009-2022. We uncovered two recent DENV-3 introductions from Asia, one of which resulted in a large outbreak in Cuba, which was previously under-reported. We also show that while outbreaks can be synchronized between islands, they are often caused by different serotypes. Our study highlights the importance of surveillance of infected travelers to provide a snapshot of local introductions and transmission in areas with limited local surveillance and suggests that the recent DENV-3 introductions may pose a major public health threat in the region.
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Affiliation(s)
- Emma Taylor-Salmon
- Department of Pediatrics, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Lauren M. Paul
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Robert T. Koch
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Afeez Sodeinde
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Joshua L. Warren
- Department of Biostatistics, Yale School of Public Health, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Sylvia Bunch
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Natalia Cano
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Marshall Cone
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Sarah Eysoldt
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Alezaundra Garcia
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Nicadia Gilles
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Andrew Hagy
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Lea Heberlein
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Rayah Jaber
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Elizabeth Kassens
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Tampa, Florida, United States of America
| | - Pamela Colarusso
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, Florida, United States of America
| | - Amanda Davis
- Bureau of Public Health Laboratories, Division of Disease Control and Health Protection, Florida Department of Health, Jacksonville, Florida, United States of America
| | - Samantha Baudin
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Edhelene Rico
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Álvaro Mejía-Echeverri
- Florida Department of Health in Miami-Dade County, Miami, Florida, United States of America
| | - Blake Scott
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Danielle Stanek
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Rebecca Zimler
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Jorge L. Muñoz-Jordán
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gilberto A. Santiago
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Laura E. Adams
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Gabriela Paz-Bailey
- Division of Vector-Borne Diseases, Centers for Disease Control and Prevention, San Juan, Puerto Rico
| | - Melanie Spillane
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Bureau for Global Health, United States Agency for International Development, Arlington, Virginia, United States of America
| | - Volha Katebi
- Office of Data, Analytics, and Technology, Division of Global Migration Health, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Robert Paulino-Ramírez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Sayira Mueses
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Armando Peguero
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Nelissa Sánchez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, UNIBE Research Hub, Santo Domingo, Dominican Republic
| | - Francesca F. Norman
- National Referral Unit for Tropical Diseases, Infectious Diseases Department, CIBER de Enfermedades Infecciosas, IRYCIS, Hospital Ramón y Cajal, Universidad de Alcalá, Madrid, Spain
| | - Juan-Carlos Galán
- Microbiology Department, Hospital Ramón y Cajal, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), CIBER de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Ralph Huits
- Department of Infectious Tropical Diseases and Microbiology, IRCCS Sacro Cuore Don Calabria Hospital, Negrar, Verona, Italy
| | - Davidson H. Hamer
- Department of Global Health, Boston University School of Public Health, Section of Infectious Diseases, Boston University School of Medicine, Center for Emerging Infectious Disease Policy and Research, Boston University, and National Emerging Infectious Disease Laboratory, Boston, Massachusetts, United States of America
| | - Chantal B.F. Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
| | - Andrea Morrison
- Bureau of Epidemiology, Division of Disease Control and Health Protection, Florida Department of Health, Tallahassee, Florida, United States of America
| | - Scott F. Michael
- Department of Biological Sciences, College of Arts and Sciences, Florida Gulf Coast University, Fort Myers, Florida, United States of America
| | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
- Public Health Modeling Unit, Yale School of Public Health, New Haven, Connecticut, United States of America
- Yale Institute for Global Health, Yale University, New Haven, Connecticut, United States of America
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America
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4
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Pagani I, Ottoboni L, Panina-Bordignon P, Martino G, Poli G, Taylor S, Turnbull JE, Yates E, Vicenzi E. Heparin Precursors with Reduced Anticoagulant Properties Retain Antiviral and Protective Effects That Potentiate the Efficacy of Sofosbuvir against Zika Virus Infection in Human Neural Progenitor Cells. Pharmaceuticals (Basel) 2023; 16:1385. [PMID: 37895856 PMCID: PMC10609960 DOI: 10.3390/ph16101385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/11/2023] [Accepted: 09/13/2023] [Indexed: 10/29/2023] Open
Abstract
Zika virus (ZIKV) infection during pregnancy can result in severe birth defects, such as microcephaly, as well as a range of other related health complications. Heparin, a clinical-grade anticoagulant, is shown to protect neural progenitor cells from death following ZIKV infection. Although heparin can be safely used during pregnancy, it retains off-target anticoagulant effects if directly employed against ZIKV infection. In this study, we investigated the effects of chemically modified heparin derivatives with reduced anticoagulant activities. These derivatives were used as experimental probes to explore the structure-activity relationships. Precursor fractions of porcine heparin, obtained during the manufacture of conventional pharmaceutical heparin with decreased anticoagulant activities, were also explored. Interestingly, these modified heparin derivatives and precursor fractions not only prevented cell death but also inhibited the ZIKV replication of infected neural progenitor cells grown as neurospheres. These effects were observed regardless of the specific sulfation position or overall charge. Furthermore, the combination of heparin with Sofosbuvir, an antiviral licensed for the treatment of hepatitis C (HCV) that also belongs to the same Flaviviridae family as ZIKV, showed a synergistic effect. This suggested that a combination therapy approach involving heparin precursors and Sofosbuvir could be a potential strategy for the prevention or treatment of ZIKV infections.
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Affiliation(s)
- Isabel Pagani
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Linda Ottoboni
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Paola Panina-Bordignon
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Gianvito Martino
- Neuroimmunology Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
| | - Guido Poli
- School of Medicine, Vita-Salute San Raffaele University, Via Olgettina 58, 20132 Milan, Italy
- Human Immuno-Virology Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
| | - Sarah Taylor
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
| | - Jeremy E Turnbull
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Edwin Yates
- Department of Biochemistry & Systems Biology, ISMIB, University of Liverpool, Liverpool L69 7ZB, UK
- Department of Life Sciences, Keele University, Keele, Staffs ST5 5BG, UK
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy
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5
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Hill V, Githinji G, Vogels CBF, Bento AI, Chaguza C, Carrington CVF, Grubaugh ND. Toward a global virus genomic surveillance network. Cell Host Microbe 2023; 31:861-873. [PMID: 36921604 PMCID: PMC9986120 DOI: 10.1016/j.chom.2023.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023]
Abstract
The COVID-19 pandemic galvanized the field of virus genomic surveillance, demonstrating its utility for public health. Now, we must harness the momentum that led to increased infrastructure, training, and political will to build a sustainable global genomic surveillance network for other epidemic and endemic viruses. We suggest a generalizable modular sequencing framework wherein users can easily switch between virus targets to maximize cost-effectiveness and maintain readiness for new threats. We also highlight challenges associated with genomic surveillance and when global inequalities persist. We propose solutions to mitigate some of these issues, including training and multilateral partnerships. Exploring alternatives to clinical sequencing can also reduce the cost of surveillance programs. Finally, we discuss how establishing genomic surveillance would aid control programs and potentially provide a warning system for outbreaks, using a global respiratory virus (RSV), an arbovirus (dengue virus), and a regional zoonotic virus (Lassa virus) as examples.
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Affiliation(s)
- Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA.
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Biochemistry and Biotechnology, Pwani University, Kilifi, Kenya
| | - Chantal B F Vogels
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Ana I Bento
- Department of Epidemiology and Biostatistics, Indiana University School of Public Health-Bloomington, Bloomington, IN, USA; The Rockefeller Foundation, New York, NY, USA
| | - Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA
| | - Christine V F Carrington
- Department of Preclinical Sciences, The University of the West Indies, St. Augustine Campus, St. Augustine, Trinidad and Tobago
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA; Yale Institute for Global Health, Yale University, New Haven, CT, USA; Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA; Public Health Modeling Unit, Yale School of Public Health, New Haven, CT, USA.
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6
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de Moraes L, Portilho MM, Vrancken B, Van den Broeck F, Santos LA, Cucco M, Tauro LB, Kikuti M, Silva MMO, Campos GS, Reis MG, Barral A, Barral-Netto M, Boaventura VS, Vandamme AM, Theys K, Lemey P, Ribeiro GS, Khouri R. Analyses of Early ZIKV Genomes Are Consistent with Viral Spread from Northeast Brazil to the Americas. Viruses 2023; 15:1236. [PMID: 37376536 DOI: 10.3390/v15061236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/19/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
The Americas, particularly Brazil, were greatly impacted by the widespread Zika virus (ZIKV) outbreak in 2015 and 2016. Efforts were made to implement genomic surveillance of ZIKV as part of the public health responses. The accuracy of spatiotemporal reconstructions of the epidemic spread relies on the unbiased sampling of the transmission process. In the early stages of the outbreak, we recruited patients exhibiting clinical symptoms of arbovirus-like infection from Salvador and Campo Formoso, Bahia, in Northeast Brazil. Between May 2015 and June 2016, we identified 21 cases of acute ZIKV infection and subsequently recovered 14 near full-length sequences using the amplicon tiling multiplex approach with nanopore sequencing. We performed a time-calibrated discrete phylogeographic analysis to trace the spread and migration history of the ZIKV. Our phylogenetic analysis supports a consistent relationship between ZIKV migration from Northeast to Southeast Brazil and its subsequent dissemination beyond Brazil. Additionally, our analysis provides insights into the migration of ZIKV from Brazil to Haiti and the role Brazil played in the spread of ZIKV to other countries, such as Singapore, the USA, and the Dominican Republic. The data generated by this study enhances our understanding of ZIKV dynamics and supports the existing knowledge, which can aid in future surveillance efforts against the virus.
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Affiliation(s)
- Laise de Moraes
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Moyra M Portilho
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Bram Vrancken
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, 1050 Bruxelles, Belgium
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Department of Biomedical Sciences, Antwerp Institute of Tropical Medicine, 2000 Antwerp, Belgium
| | - Luciane Amorim Santos
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Escola Bahiana de Medicina e Saúde Pública, Salvador 41150-100, Brazil
| | - Marina Cucco
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Laura B Tauro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Instituto de Biología Subtropical, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de Misiones, Puerto Iguazú N3370, Argentina
| | - Mariana Kikuti
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Monaise M O Silva
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Gúbio S Campos
- Laboratório de Virologia, Instituto de Ciências da Saúde, Universidade Federal da Bahia, Salvador 40231-300, Brazil
| | - Mitermayer G Reis
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Patologia e Medicina Legal, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Aldina Barral
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Manoel Barral-Netto
- Laboratório de Inflamação e Biomarcadores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
| | - Viviane Sampaio Boaventura
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Hospital Santa Izabel, Salvador 40050-410, Brazil
| | - Anne-Mieke Vandamme
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
- Center for Global Health and Tropical Medicine, Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, 1349-008 Lisbon, Portugal
| | - Kristof Theys
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
| | - Guilherme S Ribeiro
- Laboratório de Patologia e Biologia Molecular, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Departamento de Medicina Preventiva e Social, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40110-100, Brazil
| | - Ricardo Khouri
- Programa de Pós-Graduação em Ciências da Saúde, Faculdade de Medicina da Bahia, Universidade Federal da Bahia, Salvador 40026-010, Brazil
- Laboratório de Enfermidades Infecciosas Transmitidas por Vetores, Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Salvador 40296-710, Brazil
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Clinical and Epidemiological Virology, KU Leuven, 3000 Leuven, Belgium
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7
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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8
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Batovska J, Mee PT, Sawbridge TI, Rodoni BC, Lynch SE. Enhanced Arbovirus Surveillance with High-Throughput Metatranscriptomic Processing of Field-Collected Mosquitoes. Viruses 2022; 14:v14122759. [PMID: 36560765 PMCID: PMC9782886 DOI: 10.3390/v14122759] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 11/16/2022] [Accepted: 11/17/2022] [Indexed: 12/14/2022] Open
Abstract
Surveillance programs are essential for the prevention and control of mosquito-borne arboviruses that cause serious human and animal diseases. Viral metatranscriptomic sequencing can enhance surveillance by enabling untargeted, high-throughput arbovirus detection. We used metatranscriptomic sequencing to screen field-collected mosquitoes for arboviruses to better understand how metatranscriptomics can be utilised in routine surveillance. Following a significant flood event in 2016, more than 56,000 mosquitoes were collected over seven weeks from field traps set up in Victoria, Australia. The traps were split into samples of 1000 mosquitoes or less and sequenced on the Illumina HiSeq. Five arboviruses relevant to public health (Ross River virus, Sindbis virus, Trubanaman virus, Umatilla virus, and Wongorr virus) were detected a total of 33 times in the metatranscriptomic data, with 94% confirmed using reverse transcription quantitative PCR (RT-qPCR). Analysis of metatranscriptomic cytochrome oxidase I (COI) sequences enabled the detection of 12 mosquito and two biting midge species. Screening of the same traps by an established public health arbovirus surveillance program corroborated the metatranscriptomic arbovirus and mosquito species detections. Assembly of genome sequences from the metatranscriptomic data also led to the detection of 51 insect-specific viruses, both known and previously undescribed, and allowed phylogenetic comparison to past strains. We have demonstrated how metatranscriptomics can enhance surveillance by enabling untargeted arbovirus detection, providing genomic epidemiological data, and simultaneously identifying vector species from large, unsorted mosquito traps.
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Affiliation(s)
- Jana Batovska
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- Correspondence: (J.B.); (P.T.M.); Tel.: +61-3-9623-1442 (J.B.); +61-3-9032-7143 (P.T.M.)
| | - Peter T. Mee
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- Correspondence: (J.B.); (P.T.M.); Tel.: +61-3-9623-1442 (J.B.); +61-3-9032-7143 (P.T.M.)
| | - Tim I. Sawbridge
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Brendan C. Rodoni
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
| | - Stacey E. Lynch
- Agriculture Victoria Research, AgriBio Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
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9
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Stein RA, Grayon A, Katz A, Chervenak FA. The Zika virus: an opportunity to revisit reproductive health needs and disparities. Germs 2022; 12:519-537. [PMID: 38021183 PMCID: PMC10660223 DOI: 10.18683/germs.2022.1357] [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: 08/30/2022] [Revised: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 12/01/2023]
Abstract
First isolated in 1947, the Zika virus was initially connected only to limited or sporadic human infections. In late 2015, the temporal clustering of a Zika outbreak and microcephaly in newborn babies from northeastern Brazil, and the identification of a causal link between the two, led to the characterization of the congenital Zika syndrome. In the wake of the epidemic, several countries from Latin America advised women to postpone pregnancies for periods ranging from six months to two years. These recommendations initiated critical conversations about the challenges of implementing them in societies with limited access to contraception, widespread socioeconomic inequalities, and high rates of unplanned and adolescent pregnancies. The messaging targeted exclusively women, despite a high prevalence of imbalances in the relationship power, and addressed all women as a group, failing to recognize that the decision to postpone pregnancies will impact different women in different ways, depending on their age at the time. Finally, in several countries affected by the Zika epidemic, due to restrictive reproductive policies, legally terminating a pregnancy is no longer an option even at the earliest time when brain malformations as part of the congenital Zika syndrome can be detected by ultrasonography. The virus continued to circulate after 2016 in several countries. Climate change models predict an expansion of the geographical area where local Zika transmission may occur, indicating that the interface between the virus, teratogenesis, and reproductive rights is a topic of considerable interest for medicine, social sciences, and public health for years to come.
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Affiliation(s)
- Richard A. Stein
- MD, PhD, NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn 11201, NY, USA
| | - Alexis Grayon
- NYU Tandon School of Engineering, Department of Chemical and Biomolecular Engineering, 6 MetroTech Center, Brooklyn 11201, NY, USA
| | - Adi Katz
- MD, Department of Obstetrics and Gynecology, Lenox Hill Hospital, Donald and Barbara Zucker School of Medicine at Hofstra Northwell, 110 E 77th Street, New York, NY, 10075, USA
| | - Frank A. Chervenak
- MD, Department of Obstetrics and Gynecology, Lenox Hill Hospital, Donald and Barbara Zucker School of Medicine at Hofstra Northwell, 110 E 77th Street, New York, NY, 10075, USA
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10
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Porter AF, Sherry N, Andersson P, Johnson SA, Duchene S, Howden BP. New rules for genomics-informed COVID-19 responses-Lessons learned from the first waves of the Omicron variant in Australia. PLoS Genet 2022; 18:e1010415. [PMID: 36227810 PMCID: PMC9560517 DOI: 10.1371/journal.pgen.1010415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Affiliation(s)
- Ashleigh F. Porter
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Norelle Sherry
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sandra A. Johnson
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
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11
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Design of Vaccine Targeting Zika Virus Polyprotein by Immunoinformatics Technique. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10409-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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12
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Giovanetti M, Pereira LA, Adelino TÉR, Fonseca V, Xavier J, de Araújo Fabri A, Slavov SN, da Silva Lemos P, de Almeida Marques W, Kashima S, Lourenço J, de Oliveira T, Campelo de Albuquerque CF, Freitas C, Peterka CRL, da Cunha RV, Mendonça AF, Lemes da Silva V, Alcantara LCJ. A Retrospective Overview of Zika Virus Evolution in the Midwest of Brazil. Microbiol Spectr 2022; 10:e0015522. [PMID: 35254139 PMCID: PMC9045127 DOI: 10.1128/spectrum.00155-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2022] [Indexed: 11/22/2022] Open
Abstract
Since the introduction of the Zika virus (ZIKV) into Brazil in 2015, its transmission dynamics have been intensively studied in many parts of the country, although much is still unknown about its circulation in the midwestern states. Here, using nanopore technology, we obtained 23 novel partial and near-complete ZIKV genomes from the state of Goiás, located in the Midwest of Brazil. Genomic, phylogenetic, and epidemiological approaches were used to retrospectively explore the spatiotemporal evolution of the ZIKV-Asian genotype in this region. As a likely consequence of a gradual accumulation of herd immunity, epidemiological data revealed a decline in the number of reported cases over 2018 to 2021. Phylogenetic reconstructions revealed that multiple independent introductions of the Asian lineage have occurred in Goiás over time and revealed a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics. IMPORTANCE Despite the considerable morbidity and mortality of arboviral infections in Brazil, such as Zika, chikungunya, dengue fever, and yellow fever, our understanding of these outbreaks is hampered by the limited availability of genomic data to track and control the epidemic. In this study, we provide a retrospective reconstruction of the Zika virus transmission dynamics in the state of Goiás by analyzing genomic data from areas in Midwest Brazil not covered by other previous studies. Our study provides an understanding of how ZIKV initiates transmission in this region and reveals a complex transmission dynamic between epidemic seasons. Together, our results highlight the utility of genomic, epidemiological, and evolutionary methods to understand mosquito-borne epidemics, revealing how this toolkit can be used to help policymakers prioritize areas to be targeted, especially in the context of finite public health resources.
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Affiliation(s)
- Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Augusto Pereira
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | - Talita Émile Ribeiro Adelino
- Laboratório Central de Saúde Pública do Estado de Minas Gerais, Fundação Ezequiel Dias, Belo Horizonte, Minas Gerais, Brazil
| | - Vagner Fonseca
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde, Brasília, Brazil
| | - Joilson Xavier
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Allison de Araújo Fabri
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Svetoslav Nanev Slavov
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - Poliana da Silva Lemos
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Brazil
| | - William de Almeida Marques
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Simone Kashima
- University of São Paulo, Ribeirão Preto Medical School, Blood Center of Ribeirão Preto, Ribeirão Preto, São Paulo, Brazil
| | - José Lourenço
- Department of Zoology, Peter Medawar Building, University of Oxford, Oxford, UK
| | - Tulio de Oliveira
- School for Data Science and Computational Thinking, Faculty of Science and Faculty of Medicine and Health Sciences, Stellenbosch University, Stellenbosch, South Africa
| | | | - Carla Freitas
- Coordenação Geral de Laboratórios de Saúde Pública/Secretaria de Vigilância em Saúde, Ministério da Saúde (CGLAB/SVS-MS), Brasília, Brazil
| | - Cassio Roberto Leonel Peterka
- Coordenação Geral das Arboviroses, Secretaria de Vigilância em Saúde/Ministério da Saúde (CGARB/SVS-MS), Brasília, Brazil
| | | | - Ana Flávia Mendonça
- Laboratório Central de Saúde Pública Dr. Giovanni Cysneiros, Goiânia, Goiás, Brazil
| | | | - Luiz Carlos Junior Alcantara
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratório de Genética Celular e Molecular, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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13
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Abstract
6 years ago, I published a Cell Host and Microbe paper that described randomization of virus genetic populations during mosquito infection. From within the evolutionary chaos, however, there is an order that can reveal a virus' past. Using these insights, I forged a career harnessing virus evolution to understand epidemiological patterns.
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14
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Ihunwo AO, Perego J, Martino G, Vicenzi E, Panina-Bordignon P. Neurogenesis and Viral Infection. Front Immunol 2022; 13:826091. [PMID: 35251006 PMCID: PMC8891128 DOI: 10.3389/fimmu.2022.826091] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/20/2022] [Indexed: 12/26/2022] Open
Abstract
Neural stem cells (NSCs) are multipotent stem cells that reside in the fetal and adult mammalian brain, which can self-renew and differentiate into neurons and supporting cells. Intrinsic and extrinsic cues, from cells in the local niche and from distant sites, stringently orchestrates the self-renewal and differentiation competence of NSCs. Ample evidence supports the important role of NSCs in neuroplasticity, aging, disease, and repair of the nervous system. Indeed, activation of NSCs or their transplantation into injured areas of the central nervous system can lead to regeneration in animal models. Viral invasion of NSCs can negatively affect neurogenesis and synaptogenesis, with consequent cell death, impairment of cell cycle progression, early differentiation, which cause neural progenitors depletion in the cortical layer of the brain. Herein, we will review the current understanding of Zika virus (ZIKV) infection of the fetal brain and the NSCs, which are the preferential population targeted by ZIKV. Furthermore, the potential neurotropic properties of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which may cause direct neurological damage, will be discussed.
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Affiliation(s)
- Amadi Ogonda Ihunwo
- School of Anatomical Sciences, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jessica Perego
- Neuroimmunology Unit, Division of Neuroscience, San Raffaele Vita-Salute University and IRCCS San Raffaele Hospital, Milan, Italy
| | - Gianvito Martino
- Neuroimmunology Unit, Division of Neuroscience, San Raffaele Vita-Salute University and IRCCS San Raffaele Hospital, Milan, Italy
| | - Elisa Vicenzi
- Viral Pathogenesis and Biosafety Unit, Division of Immunology, Transplantation and Infectious Disesases, IRCCS San Raffaele Hospital, Milan, Italy
| | - Paola Panina-Bordignon
- Neuroimmunology Unit, Division of Neuroscience, San Raffaele Vita-Salute University and IRCCS San Raffaele Hospital, Milan, Italy
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15
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Ling Y, Cao R, Qian J, Li J, Zhou H, Yuan L, Wang Z, Ma L, Zheng G, Zhao G, Wang Z, Zhang G, Li Y. An interactive viral genome evolution network analysis system enabling rapid large-scale molecular tracing of SARS-CoV-2. Sci Bull (Beijing) 2022; 67:665-669. [PMID: 35036033 PMCID: PMC8743795 DOI: 10.1016/j.scib.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Yunchao Ling
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Ruifang Cao
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiaqiang Qian
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jiefu Li
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Haokui Zhou
- Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Liyun Yuan
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zhen Wang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Liangxiao Ma
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guangyong Zheng
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoping Zhao
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.,CAS Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guoqing Zhang
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yixue Li
- CAS Key Laboratory of Computational Biology, Bio-Med Big Data Center, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China.,Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China.,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200433, China.,School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Guangzhou Laboratory, Guangzhou 510005, China
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16
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Seabra SG, Libin PJK, Theys K, Zhukova A, Potter BI, Nebenzahl-Guimaraes H, Gorbalenya AE, Sidorov IA, Pimentel V, Pingarilho M, de Vasconcelos ATR, Dellicour S, Khouri R, Gascuel O, Vandamme AM, Baele G, Cuypers L, Abecasis AB. OUP accepted manuscript. Virus Evol 2022; 8:veac029. [PMID: 35478717 PMCID: PMC9035895 DOI: 10.1093/ve/veac029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 01/24/2022] [Accepted: 03/28/2022] [Indexed: 11/13/2022] Open
Abstract
The Zika virus (ZIKV) disease caused a public health emergency of international concern that started in February 2016. The overall number of ZIKV-related cases increased until November 2016, after which it declined sharply. While the evaluation of the potential risk and impact of future arbovirus epidemics remains challenging, intensified surveillance efforts along with a scale-up of ZIKV whole-genome sequencing provide an opportunity to understand the patterns of genetic diversity, evolution, and spread of ZIKV. However, a classification system that reflects the true extent of ZIKV genetic variation is lacking. Our objective was to characterize ZIKV genetic diversity and phylodynamics, identify genomic footprints of differentiation patterns, and propose a dynamic classification system that reflects its divergence levels. We analysed a curated dataset of 762 publicly available sequences spanning the full-length coding region of ZIKV from across its geographical span and collected between 1947 and 2021. The definition of genetic groups was based on comprehensive evolutionary dynamics analyses, which included recombination and phylogenetic analyses, within- and between-group pairwise genetic distances comparison, detection of selective pressure, and clustering analyses. Evidence for potential recombination events was detected in a few sequences. However, we argue that these events are likely due to sequencing errors as proposed in previous studies. There was evidence of strong purifying selection, widespread across the genome, as also detected for other arboviruses. A total of 50 sites showed evidence of positive selection, and for a few of these sites, there was amino acid (AA) differentiation between genetic clusters. Two main genetic clusters were defined, ZA and ZB, which correspond to the already characterized ‘African’ and ‘Asian’ genotypes, respectively. Within ZB, two subgroups, ZB.1 and ZB.2, represent the Asiatic and the American (and Oceania) lineages, respectively. ZB.1 is further subdivided into ZB.1.0 (a basal Malaysia sequence sampled in the 1960s and a recent Indian sequence), ZB.1.1 (South-Eastern Asia, Southern Asia, and Micronesia sequences), and ZB.1.2 (very similar sequences from the outbreak in Singapore). ZB.2 is subdivided into ZB.2.0 (basal American sequences and the sequences from French Polynesia, the putative origin of South America introduction), ZB.2.1 (Central America), and ZB.2.2 (Caribbean and North America). This classification system does not use geographical references and is flexible to accommodate potential future lineages. It will be a helpful tool for studies that involve analyses of ZIKV genomic variation and its association with pathogenicity and serve as a starting point for the public health surveillance and response to on-going and future epidemics and to outbreaks that lead to the emergence of new variants.
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Affiliation(s)
| | | | | | - Anna Zhukova
- Institut Pasteur, Université Paris Cité, Unité Bioinformatique Evolutive, 25-28 rue du Dr Roux, Paris F-75015, France
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, 25-28 rue du Dr Roux, Paris F-75015, France
| | | | - Hanna Nebenzahl-Guimaraes
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | | | - Victor Pimentel
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | - Marta Pingarilho
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
| | | | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Clinical and Epidemiological Virology, KU Leuven, Herestraat 49 - box 1030, Leuven 3000, Belgium
- Spatial Epidemiology Lab (SpELL), Université Libre de Bruxelles, CP 264/3, 50 av. F.D. Roosevelt, Bruxelles B-1050, Belgium
| | | | | | | | | | - Lize Cuypers
- Department of Laboratory Medicine, University Hospitals Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Ana B Abecasis
- Global Health and Tropical Medicine (GHTM), Instituto de Higiene e Medicina Tropical (IHMT), Universidade Nova de Lisboa (UNL), Rua da Junqueira 100, Lisboa 1349-008, Portugal
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17
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Santiago GA, Kalinich CC, Cruz-López F, González GL, Flores B, Hentoff A, Charriez KN, Fauver JR, Adams LE, Sharp TM, Black A, Bedford T, Ellis E, Ellis B, Waterman SH, Paz-Bailey G, Grubaugh ND, Muñoz-Jordán JL. Tracing the Origin, Spread, and Molecular Evolution of Zika Virus in Puerto Rico, 2016-2017. Emerg Infect Dis 2021; 27:2971-2973. [PMID: 34670646 PMCID: PMC8544999 DOI: 10.3201/eid2711.211575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We reconstructed the 2016-2017 Zika virus epidemic in Puerto Rico by using complete genomes to uncover the epidemic's origin, spread, and evolutionary dynamics. Our study revealed that the epidemic was propelled by multiple introductions that spread across the island, intricate evolutionary patterns, and ≈10 months of cryptic transmission.
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18
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Dudas G, Hong SL, Potter BI, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, Fuh-Neba T, Vickos U, Ulrich M, Leendertz FH, Khan K, Huber C, Watts A, Olendraitė I, Snijder J, Wijnant KN, Bonvin AMJJ, Martres P, Behillil S, Ayouba A, Maidadi MF, Djomsi DM, Godwe C, Butel C, Šimaitis A, Gabrielaitė M, Katėnaitė M, Norvilas R, Raugaitė L, Koyaweda GW, Kandou JK, Jonikas R, Nasvytienė I, Žemeckienė Ž, Gečys D, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Alzbutas G, Aziza AA, Lusamaki EK, Cigolo JCM, Mawete FM, Lofiko EL, Kingebeni PM, Tamfum JJM, Belizaire MRD, Essomba RG, Assoumou MCO, Mboringong AB, Dieng AB, Juozapaitė D, Hosch S, Obama J, Ayekaba MO, Naumovas D, Pautienius A, Rafaï CD, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Lesauskaitė V, Žemaitis L, Griškevičius L, Baele G. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nat Commun 2021; 12:5769. [PMID: 34599175 PMCID: PMC8486757 DOI: 10.1038/s41467-021-26055-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
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Affiliation(s)
- Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Barney I Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
- Viral Evolution, Robert Koch Institute, 13353, Berlin, Germany
| | - Frédéric S Niatou-Singa
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Thais B Tombolomako
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Terence Fuh-Neba
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Ulrich Vickos
- Infectious and Tropical Diseases Unit, Department of medicine, Amitié Hospital, Bangui, Central African Republic
- Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Kamran Khan
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | | | | | - Ingrida Olendraitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kim N Wijnant
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Pascale Martres
- Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
| | - Sylvie Behillil
- Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Ahidjo Ayouba
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Martin Foudi Maidadi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Dowbiss Meta Djomsi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Celestin Godwe
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Aistis Šimaitis
- The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
| | | | - Monika Katėnaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Rimvydas Norvilas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Ligita Raugaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Giscard Wilfried Koyaweda
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Jephté Kaleb Kandou
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Rimvydas Jonikas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Inga Nasvytienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Živilė Žemeckienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Dovydas Gečys
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kamilė Tamušauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Milda Norkienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Emilija Vasiliūnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Danguolė Žiogienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marius Šukys
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mantas Šarauskas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Gediminas Alzbutas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Adrienne Amuri Aziza
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Claude Makangara Cigolo
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Francisca Muyembe Mawete
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Emmanuel Lokilo Lofiko
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
| | - Placide Mbala Kingebeni
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | | | - René Ghislain Essomba
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marie Claire Okomo Assoumou
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Alle Baba Dieng
- World Health Organization, Cameroon Office, Yaoundé, Cameroon
| | - Dovilė Juozapaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Justino Obama
- Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
| | | | - Daniel Naumovas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Clotaire Donatien Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Astra Vitkauskienė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rasa Ugenskienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alma Gedvilaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Čereškevičius
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lukas Žemaitis
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Laimonas Griškevičius
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
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19
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado RR, McConnell A, Widen SG, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek TG, Menachery VD, Weaver SC, Routh AL. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. eLife 2021; 10:68479. [PMID: 34581669 PMCID: PMC8478411 DOI: 10.7554/elife.68479] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/08/2021] [Indexed: 12/13/2022] Open
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for next-generation sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called ‘Tiled-ClickSeq’, which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5’UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,ClickSeq Technologies LLC, Galveston, United States
| | - Rose M Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Patrick Newman
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Jessica A Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Kenneth S Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Aaron L Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rafael Rg Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, United States
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States
| | - Rick B Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, United States
| | - Thomas G Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Pathology, University of Texas Medical Branch, Galveston, United States
| | - Vineet D Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Scott C Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, United States.,Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States
| | - Andrew L Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, United States.,Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, United States.,Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, United States
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20
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Jaworski E, Langsjoen RM, Mitchell B, Judy B, Newman P, Plante JA, Plante KS, Miller AL, Zhou Y, Swetnam D, Sotcheff S, Morris V, Saada N, Machado R, McConnell A, Widen S, Thompson J, Dong J, Ren P, Pyles RB, Ksiazek T, Menachery VD, Weaver SC, Routh A. Tiled-ClickSeq for targeted sequencing of complete coronavirus genomes with simultaneous capture of RNA recombination and minority variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.03.10.434828. [PMID: 33758846 PMCID: PMC7987005 DOI: 10.1101/2021.03.10.434828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
High-throughput genomics of SARS-CoV-2 is essential to characterize virus evolution and to identify adaptations that affect pathogenicity or transmission. While single-nucleotide variations (SNVs) are commonly considered as driving virus adaption, RNA recombination events that delete or insert nucleic acid sequences are also critical. Whole genome targeting sequencing of SARS-CoV-2 is typically achieved using pairs of primers to generate cDNA amplicons suitable for Next-Generation Sequencing (NGS). However, paired-primer approaches impose constraints on where primers can be designed, how many amplicons are synthesized and requires multiple PCR reactions with non-overlapping primer pools. This imparts sensitivity to underlying SNVs and fails to resolve RNA recombination junctions that are not flanked by primer pairs. To address these limitations, we have designed an approach called 'Tiled-ClickSeq', which uses hundreds of tiled-primers spaced evenly along the virus genome in a single reverse-transcription reaction. The other end of the cDNA amplicon is generated by azido-nucleotides that stochastically terminate cDNA synthesis, removing the need for a paired-primer. A sequencing adaptor containing a Unique Molecular Identifier (UMI) is appended to the cDNA fragment using click-chemistry and a PCR reaction generates a final NGS library. Tiled-ClickSeq provides complete genome coverage, including the 5'UTR, at high depth and specificity to the virus on both Illumina and Nanopore NGS platforms. Here, we analyze multiple SARS-CoV-2 isolates and clinical samples to simultaneously characterize minority variants, sub-genomic mRNAs (sgmRNAs), structural variants (SVs) and D-RNAs. Tiled-ClickSeq therefore provides a convenient and robust platform for SARS-CoV-2 genomics that captures the full range of RNA species in a single, simple assay.
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Affiliation(s)
- Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- ClickSeq Technologies LLC, Galveston, TX, USA
| | - Rose M. Langsjoen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Brooke Mitchell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Barbara Judy
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Patrick Newman
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Jessica A. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Kenneth S. Plante
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Aaron L. Miller
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Yiyang Zhou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Daniele Swetnam
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Victoria Morris
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Nehad Saada
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rafael Machado
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Allan McConnell
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Steve Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jill Thompson
- Next-Generation Sequencing Core, The University of Texas Medical Branch, Galveston, TX, USA
| | - Jianli Dong
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
| | - Rick B. Pyles
- Department of Pediatrics, University of Texas Medical Branch, Galveston, TX, USA
| | - Thomas Ksiazek
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Pathology, University of Texas Medical Branch, Galveston TX, USA
| | - Vineet D. Menachery
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C. Weaver
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, TX, USA
- Department of Microbiology and Immunology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Andrew Routh
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Centre for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas, USA
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21
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The epidermal growth factor receptor is a relevant host factor in the early stages of Zika virus life cycle in vitro. J Virol 2021; 95:e0119521. [PMID: 34379506 DOI: 10.1128/jvi.01195-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Zika virus (ZIKV) is a flavivirus well-known for the epidemic in the Americas in 2015-2016, where microcephaly in newborns and other neurological complications were connected to ZIKV infection. Many aspects of the viral life cycle, including binding and entry into the host cell, are still enigmatic. Based on the observation that CHO cells lack the expression of EGFR and are not permissive for various ZIKV strains, the relevance of EGFR for the viral life cycle was analyzed. Infection of A549 cells by ZIKV leads to a rapid internalization of EGFR that colocalizes with the endosomal marker EEA1. Moreover, the infection by different ZIKV strains is associated with an activation of EGFR and subsequent activation of the MAPK/ERK signaling cascade. However, treatment of the cells with MβCD, which on the one hand leads to an activation of EGFR but on the other hand prevents EGFR internalization, impairs ZIKV infection. Specific inhibition of EGFR or of the RAS-RAF-MEK-ERK signal transduction cascade hinders ZIKV infection by inhibition of ZIKV entry. In accordance to this, knockout of EGFR expression impedes ZIKV entry. In case of an already established infection, inhibition of EGFR or of downstream signaling does not affect viral replication. Taken together, these data demonstrate the relevance of EGFR in the early stages of ZIKV infection and identify EGFR as a target for antiviral strategies. Importance These data deepen the knowledge about the ZIKV infection process and demonstrate the relevance of EGFR for ZIKV entry. In light of the fact that a variety of specific and efficient inhibitors of EGFR and of EGFR-dependent signaling were developed and licensed, repurposing of these substances could be a helpful tool to prevent the spreading of ZIKV infection in an epidemic outbreak.
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22
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African-Lineage Zika Virus Replication Dynamics and Maternal-Fetal Interface Infection in Pregnant Rhesus Macaques. J Virol 2021; 95:e0222020. [PMID: 34076485 PMCID: PMC8312872 DOI: 10.1128/jvi.02220-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Following the Zika virus (ZIKV) outbreak in the Americas, ZIKV was causally associated with microcephaly and a range of neurological and developmental symptoms, termed congenital Zika syndrome (CZS). The viruses responsible for this outbreak belonged to the Asian lineage of ZIKV. However, in vitro and in vivo studies assessing the pathogenesis of African-lineage ZIKV demonstrated that African-lineage isolates often replicated to high titers and caused more-severe pathology than Asian-lineage isolates. To date, the pathogenesis of African-lineage ZIKV in a translational model, particularly during pregnancy, has not been rigorously characterized. Here, we infected four pregnant rhesus macaques with a low-passage-number strain of African-lineage ZIKV and compared its pathogenesis to those for a cohort of four pregnant rhesus macaques infected with an Asian-lineage isolate and a cohort of mock-inoculated controls. The viral replication kinetics for the two experimental groups were not significantly different, and both groups developed robust neutralizing antibody titers above levels considered to be protective. There was no evidence of significant fetal head growth restriction or gross fetal harm at delivery (1 to 1.5 weeks prior to full term) in either group. However, a significantly higher burden of ZIKV viral RNA (vRNA) was found in the maternal-fetal interface tissues of the macaques exposed to an African-lineage isolate. Our findings suggest that ZIKV of any genetic lineage poses a threat to pregnant individuals and their infants. IMPORTANCE ZIKV was first identified in 1947 in Africa, but most of our knowledge of ZIKV is based on studies of the distinct Asian genetic lineage, which caused the outbreak in the Americas in 2015 to 2016. In its most recent update, the WHO stated that improved understanding of African-lineage ZIKV pathogenesis during pregnancy must be a priority. The recent detection of African-lineage isolates in Brazil underscores the need to understand the impact of these viruses. Here, we provide the first comprehensive assessment of African-lineage ZIKV infection during pregnancy in a translational nonhuman primate model. We show that African-lineage isolates replicate with kinetics similar to those of Asian-lineage isolates and can infect the placenta. However, there was no evidence of more-severe outcomes with African-lineage isolates. Our results highlight both the threat that African-lineage ZIKV poses to pregnant individuals and their infants and the need for epidemiological and translational in vivo studies with African-lineage ZIKV.
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23
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Sharp TM, Morris S, Morrison A, de Lima Corvino D, Santiago GA, Shieh WJ, Rico E, Kopp E, Muñoz-Jordán JL, Marttos A, Paz-Bailey G, Abbo LM, Stanek D. Fatal Dengue Acquired in Florida. N Engl J Med 2021; 384:2257-2259. [PMID: 34107186 PMCID: PMC11304554 DOI: 10.1056/nejmc2023298] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Tyler M Sharp
- Centers for Disease Control and Prevention, San Juan, PR
| | | | | | | | | | - Wun-Ju Shieh
- Centers for Disease Control and Prevention, Atlanta, GA
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24
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Repeated exposure to dengue virus elicits robust cross neutralizing antibodies against Zika virus in residents of Northeastern Thailand. Sci Rep 2021; 11:9634. [PMID: 33953258 PMCID: PMC8100282 DOI: 10.1038/s41598-021-88933-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 04/19/2021] [Indexed: 11/23/2022] Open
Abstract
Zika virus (ZIKV) and dengue virus (DENV) are antigenically related mosquito-borne flaviviruses. ZIKV is becoming increasingly prevalent in DENV-endemic regions, raising the possibility that pre-existing immunity to one virus could modulate the response to a heterologous virus, although whether this would be beneficial or detrimental is unclear. Here, we analyzed sera from residents of a DENV-endemic region of Thailand to determine the prevalence of DENV-elicited antibodies capable of cross-neutralizing ZIKV. Sixty-one participants who were asymptomatic and unselected for viral serostatus were enrolled. Among them, 52 and 51 were seropositive for IgG antibody against DENV or ZIKV E proteins (ELISA assay), respectively. Notably, 44.23% (23/52) of DENV seropositive participants had serological evidence of multiple exposures to DENV, and these subjects had strikingly higher titers and broader reactivities of neutralizing antibodies (NAbs) against ZIKV and DENV heterotypes compared with participants with serological evidence of a single DENV infection (25/52, 48.1%). In total, 17 of the 61 participants (27.9%) had NAbs against ZIKV and all four DENV serotypes, and an additional 9 (14.8%) had NAbs against ZIKV and DENV1, 2, and 3. NAbs against DENV2 were the most prevalent (44/61, 72.1%) followed by DENV3 (38/61, 62.3%) and DENV1 (36/61, 59.0%). Of note, anti-ZIKV NAbs were more prevalent than anti-DENV4 NAbs (27/61, 44.3% and 21/61, 34.4%, respectively). Primary ZIKV infection was detected in two participants, confirming that ZIKV co-circulates in this region. Thus, residents of DENV-endemic regions with repeated exposure to DENV have higher titers of NAbs against ZIKV than individuals with only a single DENV exposure.
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25
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MU, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.31.21254685. [PMID: 33851177 PMCID: PMC8043474 DOI: 10.1101/2021.03.31.21254685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
- Universidad Agraria del Ecuador
| | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Arne Kühne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | | | - Orson Mestanza
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
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26
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Giozza SP, Bermúdez XPD, Kara EO, Calvet GA, de Filippis AMB, Lacerda MVG, Bôtto-Menezes CHA, da Costa Castilho M, Franca RFO, Neto AM, Storme C, Lima NS, Modjarrad K, de Oliveira MCP, Pereira GFM, Broutet N. An initiative of cooperation in Zika virus research: the experience of the ZIKABRA study in Brazil. BMC Public Health 2021; 21:572. [PMID: 33757480 PMCID: PMC7985753 DOI: 10.1186/s12889-021-10596-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 03/09/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Zika virus outbreak has triggered a set of local and global actions for a rapid, effective, and timely public health response. A World Health Organization (WHO) initiative, supported by the Department of Chronic Condition Diseases and Sexually Transmitted Infections (DCCI) of the Health Surveillance Secretariat (SVS), Brazil Ministry of Health (MoH) and other public health funders, resulted in the start of the "Study on the persistence of Zika virus in body fluids of patients with ZIKV infection in Brazil - ZIKABRA study". The ZIKABRA study was designed to increase understanding of how long ZIKV persists in bodily fluids and informing best measures to prevent its transmission. Data collection began in July 2017 and the last follow up visit occurred in 06/26/2020. METHODS A framework for the ZIKABRA Cooperation initiative is provided through a description and analysis of the mechanisms, strategies and the ethos that have guided the models of international governance and technical cooperation in health for scientific exchange in the context of a public health emergency. Among the methodological strategies, we included a review of the legal documents that supported the ZIKABRA Cooperation; weekly documents produced in the meetings and working sessions; technical reports; memorandum of understanding and the research protocol. CONCLUSION We highlight the importance of working in cooperation between different institutional actors to achieve more significant results than that obtained by each group working in isolation. In addition, we point out the advantages of training activities, ongoing supervision, the construction of local installed research capacity, training academic and non-academic human resources, improvement of laboratory equipment, knowledge transfer and the availability of the ZIKABRA study protocol for development of similar studies, favoring the collective construction of knowledge to provide public health emergency responses. Strategy harmonization; human resources and health services; timing and recruiting particularities and processing institutional clearance in the different sites can be mentioned as challenges in this type of initiative.
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Affiliation(s)
- Silvana Pereira Giozza
- Department of Chronic Condition Diseases and Sexually Transmitted Infections, Health Surveillance Secretariat, Ministry of Health, Brazil, SRTVN Quadra 701, Lote D, Edifício PO700 - 5° andar, Brasília, Distrito Federal, 70719-040, Brazil.
| | | | | | | | | | | | | | | | | | | | - Casey Storme
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Noemia S Lima
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD, USA
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, USA
| | - Maria Cristina Pimenta de Oliveira
- Department of Chronic Condition Diseases and Sexually Transmitted Infections, Health Surveillance Secretariat, Ministry of Health, Brazil, SRTVN Quadra 701, Lote D, Edifício PO700 - 5° andar, Brasília, Distrito Federal, 70719-040, Brazil
| | - Gerson Fernando Mendes Pereira
- Department of Chronic Condition Diseases and Sexually Transmitted Infections, Health Surveillance Secretariat, Ministry of Health, Brazil, SRTVN Quadra 701, Lote D, Edifício PO700 - 5° andar, Brasília, Distrito Federal, 70719-040, Brazil
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27
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Henderson AD, Kama M, Aubry M, Hue S, Teissier A, Naivalu T, Bechu VD, Kailawadoko J, Rabukawaqa I, Sahukhan A, Hibberd ML, Nilles EJ, Funk S, Whitworth J, Watson CH, Lau CL, Edmunds WJ, Cao-Lormeau VM, Kucharski AJ. Interactions between timing and transmissibility explain diverse flavivirus dynamics in Fiji. Nat Commun 2021; 12:1671. [PMID: 33723237 PMCID: PMC7961049 DOI: 10.1038/s41467-021-21788-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 02/10/2021] [Indexed: 12/14/2022] Open
Abstract
Zika virus (ZIKV) has caused large, brief outbreaks in isolated populations, however ZIKV can also persist at low levels over multiple years. The reasons for these diverse transmission dynamics remain poorly understood. In Fiji, which has experienced multiple large single-season dengue epidemics, there was evidence of multi-year transmission of ZIKV between 2013 and 2017. To identify factors that could explain these differences in dynamics between closely related mosquito-borne flaviviruses, we jointly fit a transmission dynamic model to surveillance, serological and molecular data. We estimate that the observed dynamics of ZIKV were the result of two key factors: strong seasonal effects, which created an ecologically optimal time of year for outbreaks; and introduction of ZIKV after this optimal time, which allowed ZIKV transmission to persist over multiple seasons. The ability to jointly fit to multiple data sources could help identify a similar range of possible outbreak dynamics in other settings.
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Affiliation(s)
- Alasdair D Henderson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - Mike Kama
- Fiji Center for Diseases Control, Suva, Fiji
| | - Maite Aubry
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | - Stephane Hue
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Anita Teissier
- Institut Louis Malardé, Papeete, Tahiti, French Polynesia
| | | | | | | | | | | | - Martin L Hibberd
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Sebastian Funk
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Jimmy Whitworth
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.,Epidemic Diseases Research Group Oxford, University of Oxford, Oxford, UK
| | - Colleen L Lau
- Research School of Population Health, The Australian National University, Canberra, ACT, Australia
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Adam J Kucharski
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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28
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Genomic and Epidemiological Surveillance of Zika Virus in the Amazon Region. Cell Rep 2021; 30:2275-2283.e7. [PMID: 32075736 DOI: 10.1016/j.celrep.2020.01.085] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 12/16/2019] [Accepted: 01/24/2020] [Indexed: 02/08/2023] Open
Abstract
Zika virus (ZIKV) has caused an explosive epidemic linked to severe clinical outcomes in the Americas. As of June 2018, 4,929 ZIKV suspected infections and 46 congenital syndrome cases had been reported in Manaus, Amazonas, Brazil. Although Manaus is a key demographic hub in the Amazon region, little is known about the ZIKV epidemic there, in terms of both transmission and viral genetic diversity. Using portable virus genome sequencing, we generated 59 ZIKV genomes in Manaus. Phylogenetic analyses indicated multiple introductions of ZIKV from northeastern Brazil to Manaus. Spatial genomic analysis of virus movement among six areas in Manaus suggested that populous northern neighborhoods acted as sources of virus transmission to other neighborhoods. Our study revealed how the ZIKV epidemic was ignited and maintained within the largest urban metropolis in the Amazon. These results might contribute to improving the public health response to outbreaks in Brazil.
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Li SL, Messina JP, Pybus OG, Kraemer MUG, Gardner L. A review of models applied to the geographic spread of Zika virus. Trans R Soc Trop Med Hyg 2021; 115:956-964. [PMID: 33570155 PMCID: PMC8417088 DOI: 10.1093/trstmh/trab009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 12/13/2020] [Accepted: 01/08/2021] [Indexed: 11/13/2022] Open
Abstract
In recent years, Zika virus (ZIKV) has expanded its geographic range and in 2015–2016 caused a substantial epidemic linked to a surge in developmental and neurological complications in newborns. Mathematical models are powerful tools for assessing ZIKV spread and can reveal important information for preventing future outbreaks. We reviewed the literature and retrieved modelling studies that were developed to understand the spatial epidemiology of ZIKV spread and risk. We classified studies by type, scale, aim and applications and discussed their characteristics, strengths and limitations. We examined the main objectives of these models and evaluated the effectiveness of integrating epidemiological and phylogeographic data, along with socioenvironmental risk factors that are known to contribute to vector–human transmission. We also assessed the promising application of human mobility data as a real-time indicator of ZIKV spread. Lastly, we summarised model validation methods used in studies to ensure accuracy in models and modelled outcomes. Models are helpful for understanding ZIKV spread and their characteristics should be carefully considered when developing future modelling studies to improve arbovirus surveillance.
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Affiliation(s)
- Sabrina L Li
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK
| | - Jane P Messina
- School of Geography and the Environment, University of Oxford, South Parks Road, Oxford, OX1 3QY, UK.,School of Global and Area Studies, University of Oxford, 12 Bevington Road, Oxford, OX2 6LH, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, 11a Mansfield Rd, Oxford, OX1 3SZ, UK
| | - Lauren Gardner
- Department of Civil and Systems Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA.,Center for Systems Science and Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218-2682, USA
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Abstract
Background: In the past 5 years, the Zika virus (ZIKV) has gone from being associated with mild infection to one of the most studied viruses worldwide. Between 2015 and 2016, the first reports of pregnant women with confirmed and/or suspected ZIKV infection described fetuses and newborns with severe congenital malformations, in particular microcephaly and central nervous system malformations, leading to a strong suspicion of its association with the virus. Despite all the knowledge rapidly acquired since the beginning of the ZIKV outbreak, many questions are still to be answered and further studies on the infection and its consequences are required.Aim: To present the currently available evidence on the epidemiological and clinical aspects of ZIKV infection.Methods: Non-systematic review carried out in MEDLINE (PubMed), LILACS (VHL), Scopus, Web of Science, Cochrane and CAPES Portal databases for the past five years using the search terms arboviruses, flavivirus, Zika and ZIKV.Results: The acute clinical of ZIKV infection in children seems very similar to that in adults, with fever (usully low), rash maculopapular and pruritus. Neurological complication associated with ZIKV reported in the literature include Guillain-Barré syndrome and meningoencephalitis. More recently, the term congenital Zika syndrome (CZS) has been adopted to describe a set of symptoms and signs in children whose mothers had ZIKV infection confirmed during pregnancy.Conclusions: More detailed knowledge of ZIKV infection in children allows the pediatrician to diagnose earlier, implement the correct treatment, monitor warnings signs for the most severe forms, and especially establish effective preventive measures.Abbreviations:: CDC, Centers for Disease Control; CZS, congenital Zika syndrome; DEET, N, N-diethyl-3-methylbenzamide; GBS, Guillain-Barré syndrome; PRNT, plaque reduction neutralisation test; RNA, ribonucleic acid; RT-PCR, reverse transcriptase polymerase chain reaction; STX, saxitoxin; ZIKV, Zika virus.
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Affiliation(s)
- Marlos Melo Martins
- Department of Pediatrics, Institute of Childcare and Pediatrics Martagão Gesteira, Federal University of Rio De Janeiro, Rio De Janeiro, Brazil
| | - Roberto De Andrade Medronho
- Department of Epidemiology and Public Health, School of Medicine, Federal University of Rio De Janeiro, Rio De Janeiro, Brazil
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Zika Virus Infection Leads to Demyelination and Axonal Injury in Mature CNS Cultures. Viruses 2021; 13:v13010091. [PMID: 33440758 PMCID: PMC7827345 DOI: 10.3390/v13010091] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 12/16/2020] [Accepted: 12/24/2020] [Indexed: 01/03/2023] Open
Abstract
Understanding how Zika virus (Flaviviridae; ZIKV) affects neural cells is paramount in comprehending pathologies associated with infection. Whilst the effects of ZIKV in neural development are well documented, impact on the adult nervous system remains obscure. Here, we investigated the effects of ZIKV infection in established mature myelinated central nervous system (CNS) cultures. Infection incurred damage to myelinated fibers, with ZIKV-positive cells appearing when myelin damage was first detected as well as axonal pathology, suggesting the latter was a consequence of oligodendroglia infection. Transcriptome analysis revealed host factors that were upregulated during ZIKV infection. One such factor, CCL5, was validated in vitro as inhibiting myelination. Transferred UV-inactivated media from infected cultures did not damage myelin and axons, suggesting that viral replication is necessary to induce the observed effects. These data show that ZIKV infection affects CNS cells even after myelination-which is critical for saltatory conduction and neuronal function-has taken place. Understanding the targets of this virus across developmental stages including the mature CNS, and the subsequent effects of infection of cell types, is necessary to understand effective time frames for therapeutic intervention.
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Petrone ME, Earnest R, Lourenço J, Kraemer MUG, Paulino-Ramirez R, Grubaugh ND, Tapia L. Asynchronicity of endemic and emerging mosquito-borne disease outbreaks in the Dominican Republic. Nat Commun 2021; 12:151. [PMID: 33420058 PMCID: PMC7794562 DOI: 10.1038/s41467-020-20391-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/27/2020] [Indexed: 12/21/2022] Open
Abstract
Mosquito-borne viruses threaten the Caribbean due to the region's tropical climate and seasonal reception of international tourists. Outbreaks of chikungunya and Zika have demonstrated the rapidity with which these viruses can spread. Concurrently, dengue fever cases have climbed over the past decade. Sustainable disease control measures are urgently needed to quell virus transmission and prevent future outbreaks. Here, to improve upon current control methods, we analyze temporal and spatial patterns of chikungunya, Zika, and dengue outbreaks reported in the Dominican Republic between 2012 and 2018. The viruses that cause these outbreaks are transmitted by Aedes mosquitoes, which are sensitive to seasonal climatological variability. We evaluate whether climate and the spatio-temporal dynamics of dengue outbreaks could explain patterns of emerging disease outbreaks. We find that emerging disease outbreaks were robust to the climatological and spatio-temporal constraints defining seasonal dengue outbreak dynamics, indicating that constant surveillance is required to prevent future health crises.
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Affiliation(s)
- Mary E Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA.
| | - Rebecca Earnest
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - José Lourenço
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | | | - Robert Paulino-Ramirez
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, Santo Domingo, Dominican Republic
| | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, 06510, USA
| | - Leandro Tapia
- Instituto de Medicina Tropical & Salud Global, Universidad Iberoamericana, Santo Domingo, Dominican Republic.
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Candido DDS, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, De Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, Du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Virus Evol 2021; 7:veab051. [PMID: 34527281 PMCID: PMC8244811 DOI: 10.1093/ve/veab051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil 090613, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil 090112, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Domenica De Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Anna-Lena Sander
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | | | - Orson Mestanza
- Servicio de Genética, Instituto Nacional de Salud del Niño San Borja, Lima 15037, Perú
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Louis Du Plessis
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JW, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
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McBroom K. A Comparison of Zika Virus and COVID-19: Clinical Overview and Public Health Messaging. J Midwifery Womens Health 2021; 66:334-342. [PMID: 34096682 PMCID: PMC8242848 DOI: 10.1111/jmwh.13230] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 02/13/2021] [Accepted: 02/20/2021] [Indexed: 12/30/2022]
Abstract
Prenatal exposure to the Zika virus (ZIKV) is associated with a significant risk of neurological impairment for infants. ZIKV serves as a cautionary model with significant parallels to the current coronavirus 2019 (COVID-19) pandemic. A limited literature search was performed to compare and contrast the clinical and psychosocial aspects of infection with ZIKV and COVID-19. There are significant parallels between ZIKV disease and COVID-19 in terms of limited diagnostic techniques, therapeutics, and prognostic uncertainties. Both infections are associated with a significant risk of adverse outcomes for either the pregnant individual or the fetus. Existing social and economic inequalities amplify the risk burden of ZIKV disease and COVID-19 in vulnerable communities. Although each pathogen has unique features, there are underlying common principles with regard to the recognition, communication, and mitigation of risk of infection. Misinformation spread by social media platforms has undermined public health efforts and patient adoption of recommended mitigation strategies. Health care providers can provide partnership, social support, and evidence-based information to enhance health-seeking behaviors, thereby minimizing the risks for pregnant and reproductive-aged persons.
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Affiliation(s)
- Kelly McBroom
- College of NursingSeattle UniversitySeattleWashington
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Osman S, Preet R. Dengue, chikungunya and Zika in GeoSentinel surveillance of international travellers: a literature review from 1995 to 2020. J Travel Med 2020; 27:6007546. [PMID: 33258476 DOI: 10.1093/jtm/taaa222] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION GeoSentinel is a global surveillance network of travel medicine providers seeing ill-returned travellers. Much of our knowledge on health problems and infectious encountered by international travellers has evolved as a result of GeoSentinel surveillance, providing geographic and temporal trends in morbidity among travellers while contributing to improved pre-travel advice. We set out to synthesize epidemiological information, clinical manifestations and time trends for dengue, chikungunya and Zika in travellers as captured by GeoSentinel. METHODS We conducted a systematic literature search in PubMed on international travellers who presented with dengue, chikungunya or Zika virus infections to GeoSentinel sites around the world from 1995 until 2020. RESULTS Of 107 GeoSentinel publications, 42 articles were related to dengue, chikungunya and/or Zika. The final analyses and synthesis of and results presented here are based on the findings from 27 original articles covering the three arboviral diseases. CONCLUSIONS Dengue is the most frequent arboviral disease encountered in travellers presenting to GeoSentinel sites, with increasing trends over the past two decades. In Southeast Asia, annual proportionate morbidity increased from 50 dengue cases per 1000 ill returned travellers in non-epidemic years to an average of 159 cases per 1000 travellers during epidemic years. The highest number of travellers with chikungunya virus infections was reported during the chikungunya outbreak in the Americas and the Caribbean in the years 2013-16. Zika was first reported by GeoSentinel already in 2012, but notifications peaked in the years 2016-17 reflecting the public health emergency in the Americas at the time.
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Affiliation(s)
- S Osman
- Department of Epidemiology and Global Health, Faculty of Medicine, Umeå University, Umeå, 90185, Sweden
| | - R Preet
- Department of Epidemiology and Global Health, Faculty of Medicine, Umeå University, Umeå, 90185, Sweden
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Sun H, Dickens BL, Jit M, Cook AR, Carrasco LR. Mapping the cryptic spread of the 2015-2016 global Zika virus epidemic. BMC Med 2020; 18:399. [PMID: 33327961 PMCID: PMC7744256 DOI: 10.1186/s12916-020-01845-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 11/06/2020] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Zika virus (ZIKV) emerged as a global epidemic in 2015-2016 from Latin America with its true geographical extent remaining unclear due to widely presumed underreporting. The identification of locations with potential and unknown spread of ZIKV is a key yet understudied component for outbreak preparedness. Here, we aim to identify locations at a high risk of cryptic ZIKV spread during 2015-2016 to further the understanding of the global ZIKV epidemiology, which is critical for the mitigation of the risk of future epidemics. METHODS We developed an importation simulation model to estimate the weekly number of ZIKV infections imported in each susceptible spatial unit (i.e. location that did not report any autochthonous Zika cases during 2015-2016), integrating epidemiological, demographic, and travel data as model inputs. Thereafter, a global risk model was applied to estimate the weekly ZIKV transmissibility during 2015-2016 for each location. Finally, we assessed the risk of onward ZIKV spread following importation in each susceptible spatial unit to identify locations with a high potential for cryptic ZIKV spread during 2015-2016. RESULTS We have found 24 susceptible spatial units that were likely to have experienced cryptic ZIKV spread during 2015-2016, of which 10 continue to have a high risk estimate within a highly conservative scenario, namely, Luanda in Angola, Banten in Indonesia, Maharashtra in India, Lagos in Nigeria, Taiwan and Guangdong in China, Dakar in Senegal, Maputo in Mozambique, Kinshasa in Congo DRC, and Pool in Congo. Notably, among the 24 susceptible spatial units identified, some have reported their first ZIKV outbreaks since 2017, thus adding to the credibility of our results (derived using 2015-2016 data only). CONCLUSION Our study has provided valuable insights into the potentially high-risk locations for cryptic ZIKV circulation during the 2015-2016 pandemic and has also laid a foundation for future studies that attempt to further narrow this key knowledge gap. Our modelling framework can be adapted to identify areas with likely unknown spread of other emerging vector-borne diseases, which has important implications for public health readiness especially in resource-limited settings.
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Affiliation(s)
- Haoyang Sun
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, Singapore, 117549, Republic of Singapore.
| | - Borame L Dickens
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, Singapore, 117549, Republic of Singapore
| | - Mark Jit
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
- Modelling and Economics Unit, Public Health England, London, UK
| | - Alex R Cook
- Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, Singapore, 117549, Republic of Singapore.
| | - L Roman Carrasco
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Republic of Singapore
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Ireland DDC, Manangeeswaran M, Lewkowicz AP, Engel K, Clark SM, Laniyan A, Sykes J, Lee HN, McWilliams IL, Kelley-Baker L, Tonelli LH, Verthelyi D. Long-term persistence of infectious Zika virus: Inflammation and behavioral sequela in mice. PLoS Pathog 2020; 16:e1008689. [PMID: 33301527 PMCID: PMC7728251 DOI: 10.1371/journal.ppat.1008689] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022] Open
Abstract
The neurodevelopmental defects associated with ZIKV infections early in pregnancy are well documented, however the potential defects and long-term consequences associated with milder infections in late pregnancy and perinatal period are less well understood. To model these, we challenged 1 day old (P1) immunocompetent C57BL/6 mice with ZIKV. The animals developed a transient neurological syndrome including unsteady gait, kinetic tremors, severe ataxia and seizures 10-15 days post-infection (dpi) but symptoms subsided after a week, and most animals survived. Despite apparent recovery, MRI of convalescent mice show reduced cerebellar volume that correlates with altered coordination and motor function as well as hyperactivity and impulsivity. Persistent mRNA levels of pro-inflammatory genes including Cd80, Il-1α, and Ifn-γ together with Cd3, Cd8 and perforin (PrfA), suggested persistence of low-grade inflammation. Surprisingly, the brain parenchyma of convalescent mice harbor multiple small discrete foci with viral antigen, active apoptotic processes in neurons, and cellular infiltrates, surrounded by activated astrocytes and microglia as late as 1-year post-infection. Detection of negative-sense strand viral RNA and isolation of infectious virus derived from these convalescent mice by blinded passage in Vero cells confirmed long-term persistence of replicating ZIKV in CNS of convalescent mice. Although the infection appears to persist in defined reservoirs within CNS, the resulting inflammation could increase the risk of neurodegenerative disorders. This raises concern regarding possible long-term effects in asymptomatic children exposed to the virus and suggests that long-term neurological and behavioral monitoring as well as anti-viral treatment to clear virus from the CNS may be useful in patients exposed to ZIKV at an early age.
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Affiliation(s)
- Derek D. C. Ireland
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Mohanraj Manangeeswaran
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Aaron P. Lewkowicz
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Kaliroi Engel
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Sarah M. Clark
- University of Maryland School of Medicine, Department of Psychiatry, Baltimore, Maryland, United States of America
| | - Adelle Laniyan
- University of Maryland School of Medicine, Department of Psychiatry, Baltimore, Maryland, United States of America
| | - Jacob Sykes
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Ha-Na Lee
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Ian L. McWilliams
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Logan Kelley-Baker
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
| | - Leonardo H. Tonelli
- University of Maryland School of Medicine, Department of Psychiatry, Baltimore, Maryland, United States of America
| | - Daniela Verthelyi
- US Food and Drug Administration, Office of Biotechnology Products, Silver Spring, Maryland, United States of America
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Vannella KM, Stein S, Connelly M, Swerczek J, Amaro-Carambot E, Coyle EM, Babyak A, Winkler CW, Saturday G, Gai ND, Hammoud DA, Dowd KA, Valencia LP, Ramos-Benitez MJ, Kindrachuk J, Pierson TC, Peterson KE, Brenchley JM, Whitehead SS, Khurana S, Herbert R, Chertow DS. Nonhuman primates exposed to Zika virus in utero are not protected against reinfection at 1 year postpartum. Sci Transl Med 2020; 12:eaaz4997. [PMID: 33115950 PMCID: PMC11256112 DOI: 10.1126/scitranslmed.aaz4997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/08/2020] [Indexed: 12/14/2022]
Abstract
There is limited information about the impact of Zika virus (ZIKV) exposure in utero on the anti-ZIKV immune responses of offspring. We infected six rhesus macaque dams with ZIKV early or late in pregnancy and studied four of their offspring over the course of a year postpartum. Despite evidence of ZIKV exposure in utero, we observed no structural brain abnormalities in the offspring. We detected infant-derived ZIKV-specific immunoglobulin A antibody responses and T cell memory responses during the first year postpartum in the two offspring born to dams infected with ZIKV early in pregnancy. Critically, although the infants had acquired some immunological memory of ZIKV, it was not sufficient to protect them against reinfection with ZIKV at 1 year postpartum. The four offspring reexposed to ZIKV at 1 year postpartum all survived but exhibited acute viremia and viral tropism to lymphoid tissues; three of four reexposed offspring exhibited spinal cord pathology. These data suggest that macaque infants born to dams infected with ZIKV during pregnancy remain susceptible to postnatal infection and consequent neuropathology.
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Affiliation(s)
- Kevin M Vannella
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sydney Stein
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Mark Connelly
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Joanna Swerczek
- Experimental Primate Virology Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Poolesville, MD 20837, USA
| | - Emerito Amaro-Carambot
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Elizabeth M Coyle
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Ashley Babyak
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Clayton W Winkler
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Greg Saturday
- Rocky Mountain Veterinary Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Neville D Gai
- Center for Infectious Disease Imaging, Radiology and Imaging Services, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dima A Hammoud
- Center for Infectious Disease Imaging, Radiology and Imaging Services, National Institutes of Health, Bethesda, MD 20892, USA
| | - Kimberly A Dowd
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Luis Perez Valencia
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Marcos J Ramos-Benitez
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jason Kindrachuk
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Laboratory of Emerging Viruses, Department of Medical Microbiology, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Theodore C Pierson
- Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Karin E Peterson
- Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT 59840, USA
| | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Viral Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Steve S Whitehead
- Laboratory of Infectious Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Surender Khurana
- Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20993, USA
| | - Richard Herbert
- Experimental Primate Virology Section, Comparative Medicine Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Poolesville, MD 20837, USA
| | - Daniel S Chertow
- Emerging Pathogens Section, Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD 20892, USA.
- Laboratory of Immunoregulation, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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Lemey P, Hong SL, Hill V, Baele G, Poletto C, Colizza V, O'Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history and unsampled diversity in Bayesian phylogeographic inference of SARS-CoV-2. Nat Commun 2020; 11:5110. [PMID: 33037213 PMCID: PMC7547076 DOI: 10.1038/s41467-020-18877-9] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 09/17/2020] [Indexed: 12/21/2022] Open
Abstract
Spatiotemporal bias in genome sampling can severely confound discrete trait phylogeographic inference. This has impeded our ability to accurately track the spread of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, despite the availability of unprecedented numbers of SARS-CoV-2 genomes. Here, we present an approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2. We demonstrate that including travel history data yields i) more realistic hypotheses of virus spread and ii) higher posterior predictive accuracy compared to including only sampling location. We further explore methods to ameliorate the impact of sampling bias by augmenting the phylogeographic analysis with lineages from undersampled locations. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts.
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Affiliation(s)
- Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d'Epidémiologie et de Santé Publique IPLESP, F75012, Paris, France
| | - Áine O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Kristian G Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA, 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Martha I Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Marc A Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, 90095, USA.
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Maljkovic Berry I, Rutvisuttinunt W, Voegtly LJ, Prieto K, Pollett S, Cer RZ, Kugelman JR, Bishop-Lilly KA, Morton L, Waitumbi J, Jarman RG. A Department of Defense Laboratory Consortium Approach to Next Generation Sequencing and Bioinformatics Training for Infectious Disease Surveillance in Kenya. Front Genet 2020; 11:577563. [PMID: 33101395 PMCID: PMC7546821 DOI: 10.3389/fgene.2020.577563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/31/2020] [Indexed: 11/30/2022] Open
Abstract
Epidemics of emerging and re-emerging infectious diseases are a danger to civilian and military populations worldwide. Health security and mitigation of infectious disease threats is a priority of the United States Government and the Department of Defense (DoD). Next generation sequencing (NGS) and Bioinformatics (BI) enhances traditional biosurveillance by providing additional data to understand transmission, identify resistance and virulence factors, make predictions, and update risk assessments. As more and more laboratories adopt NGS and BI technologies they encounter challenges in building local capacity. In addition to choosing the right sequencing platform and approach, considerations must also be made for the complexity of bioinformatics analyses, data storage, as well as personnel and computational requirements. To address these needs, a comprehensive training program was developed covering wet lab and bioinformatics approaches to NGS. The program is meant to be modular and adaptive to meet both common and individualized needs of medical research and public health laboratories across the DoD. The training program was first deployed internationally to the Basic Science Laboratory of the US Army Medical Research Directorate-Africa in Kisumu, Kenya, which is an overseas Lab of the Walter Reed Army Institute of Research (WRAIR). A week-long workshop with intensive focus on targeted sequencing and the bioinformatics of genome assembly (n = 24 participants) was held. Post-workshop self-assessment (completed by 21 participants) noted significant median gains in knowledge domains related to NGS targeted sequencing, bioinformatics for genome assembly, and sequence quality assessment. The participants also reported that the information on study design, sample preparation, sequencing quality control, data quality assessment, reporting, and basic and advanced bioinformatics analysis were the most useful information presented in the training. While longer-term evaluations are planned, the training resulted in significant short-term improvement of a laboratory’s self-reported wet lab and bioinformatics capabilities. This framework can be used for future DoD laboratory development in the area of NGS and BI for infectious disease surveillance, ultimately enhancing this global DoD capability.
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Affiliation(s)
- Irina Maljkovic Berry
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Wiriya Rutvisuttinunt
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States.,Office of Genomics and Advanced Technologies National Institute of Allergy and Infectious Diseases, Bethesda, MD, United States
| | - Logan J Voegtly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Karla Prieto
- College of Public Health, University of Nebraska Medical Center, Omaha, NE, United States.,Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Simon Pollett
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
| | - Regina Z Cer
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States.,Leidos, Reston, VA, United States
| | - Jeffrey R Kugelman
- Center for Genomic Studies, United States Army Medical Research Institute for Infectious Diseases, Frederick, MD, United States
| | - Kimberly A Bishop-Lilly
- Genomics & Bioinformatics Department, Biological Defense Research Directorate, Naval Medical Research Center-Frederick, Fort Detrick, MD, United States
| | - Lindsay Morton
- Global Emerging Infections Surveillance, Armed Forces Health Surveillance Branch, Silver Spring, MD, United States
| | - John Waitumbi
- Basic Science Laboratory, US Army Medical Research Directorate-Africa/Kenya Medical Research Institute, Kisumu, Kenya
| | - Richard G Jarman
- Viral Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD, United States
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Smith RC. Highlights in Medical Entomology, 2019: Familiar Foes and New Frontiers. JOURNAL OF MEDICAL ENTOMOLOGY 2020; 57:1349-1353. [PMID: 32667035 PMCID: PMC7716807 DOI: 10.1093/jme/tjaa120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Indexed: 06/11/2023]
Abstract
The 2019 Entomological Society of America annual meeting was held in St. Louis, Missouri, just blocks away from the iconic Gateway Arch. Representing a 'gateway to the West', this inspired the theme of the Highlights in Medical Entomology to reflect on the accomplishments of the past year as we move into a 'new frontier' of vector biology research. Papers were selected broadly across arthropods that influence public health, focusing on topics ranging from West Nile virus transmission, ticks and tick-borne disease, to advances in genetics and 'big data' studies. This included current perspectives on West Nile virus ecology and epidemiology, which has now been endemic in the United States for 20 yr. Additional topics such as the advantages of citizen science and the importance of scientific communication were also discussed. Together, these papers demonstrate the achievements of the vector community while emphasizing the challenges that we collectively face to reduce the burden of vector-borne disease.
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Affiliation(s)
- Ryan C Smith
- Department of Entomology, Iowa State University, Ames, IA
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Xing M, Ji M, Hu J, Zhu T, Chen Y, Bai X, Mwangi J, Mo G, Lai R, Jin L. Snake Cathelicidin Derived Peptide Inhibits Zika Virus Infection. Front Microbiol 2020; 11:1871. [PMID: 32849457 PMCID: PMC7417475 DOI: 10.3389/fmicb.2020.01871] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/16/2020] [Indexed: 01/19/2023] Open
Abstract
Zika virus (ZIKV) is a mosquito-borne virus belonging to the genus Flavivirus and has reemerged in recent years with epidemic potential. ZIKV infection may result in severe syndromes such as neurological complications and microcephaly in newborns. Therefore, ZIKV has become a global public health threat and currently there is no approved specific drug for its treatment. Animal venoms are important resources of novel drugs. Cathelicidin-BF (BF-30) is a defensive peptide identified from Bungarus fasciatus snake venom and has been shown to be an excellent template for applicable peptide design. In this study, we found that ZY13, one of the peptidic analogs of BF-30, inhibits ZIKV infection in vitro and in vivo. Mechanistic studies revealed that ZY13 can directly inactivate ZIKV and reduce the production of infectious virions. Further studies also indicated that administration of ZY13 strengthen the host antiviral immunity via AXL-SOCS (suppressor of cytokine signaling protein) pathway. Additionally, the results of mouse experiment suggest that ZY13 efficiently restrict ZIKV infection and improve the growth defects of ZIKV-infected mouse pups. Together, our findings not only demonstrate that ZY13 might be a candidate for anti-ZIKV drug, but also indicated the importance of animal venom peptides as templates for antivirals development.
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Affiliation(s)
- Meichen Xing
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mengyao Ji
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jingmei Hu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tengyu Zhu
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yaoyao Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xuewei Bai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - James Mwangi
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-African Joint Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Guoxiang Mo
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ren Lai
- College of Life Sciences, Nanjing Agricultural University, Nanjing, China
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Sino-African Joint Research Center, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China
- KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Institute for Drug Discovery and Development, Chinese Academy of Sciences, Shanghai, China
| | - Lin Jin
- Key Laboratory of Animal Models and Human Disease Mechanisms, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Key Laboratory of Bioactive Peptides of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
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Lequime S, Bastide P, Dellicour S, Lemey P, Baele G. nosoi: A stochastic agent-based transmission chain simulation framework in r. Methods Ecol Evol 2020; 11:1002-1007. [PMID: 32983401 PMCID: PMC7496779 DOI: 10.1111/2041-210x.13422] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/13/2020] [Indexed: 12/22/2022]
Abstract
The transmission process of an infectious agent creates a connected chain of hosts linked by transmission events, known as a transmission chain. Reconstructing transmission chains remains a challenging endeavour, except in rare cases characterized by intense surveillance and epidemiological inquiry. Inference frameworks attempt to estimate or approximate these transmission chains but the accuracy and validity of such methods generally lack formal assessment on datasets for which the actual transmission chain was observed.We here introduce nosoi, an open-source r package that offers a complete, tunable and expandable agent-based framework to simulate transmission chains under a wide range of epidemiological scenarios for single-host and dual-host epidemics. nosoi is accessible through GitHub and CRAN, and is accompanied by extensive documentation, providing help and practical examples to assist users in setting up their own simulations.Once infected, each host or agent can undergo a series of events during each time step, such as moving (between locations) or transmitting the infection, all of these being driven by user-specified rules or data, such as travel patterns between locations. nosoi is able to generate a multitude of epidemic scenarios, that can-for example-be used to validate a wide range of reconstruction methods, including epidemic modelling and phylodynamic analyses. nosoi also offers a comprehensive framework to leverage empirically acquired data, allowing the user to explore how variations in parameters can affect epidemic potential. Aside from research questions, nosoi can provide lecturers with a complete teaching tool to offer students a hands-on exploration of the dynamics of epidemiological processes and the factors that impact it. Because the package does not rely on mathematical formalism but uses a more intuitive algorithmic approach, even extensive changes of the entire model can be easily and quickly implemented.
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Affiliation(s)
- Sebastian Lequime
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
- Cluster of Microbial EcologyGroningen Institute for Evolutionary Life SciencesUniversity of GroningenGroningenThe Netherlands
| | - Paul Bastide
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
- IMAGCNRSUniversity of MontpellierMontpellierFrance
| | - Simon Dellicour
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
- Spatial Epidemiology Lab (SpELL)Université Libre de BruxellesBrusselsBelgium
| | - Philippe Lemey
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
| | - Guy Baele
- Department of Microbiology, Immunology and TransplantationRega InstituteKU LeuvenLeuvenBelgium
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Angelo KM, Stoney RJ, Brun-Cottan G, Leder K, Grobusch MP, Hochberg N, Kuhn S, Bottieau E, Schlagenhauf P, Chen L, Hynes NA, Perez CP, Mockenhaupt FP, Molina I, Crespillo-Andújar C, Malvy D, Caumes E, Plourde P, Shaw M, McCarthy AE, Piper-Jenks N, Connor BA, Hamer DH, Wilder-Smith A. Zika among international travellers presenting to GeoSentinel sites, 2012-2019: implications for clinical practice. J Travel Med 2020; 27:5824831. [PMID: 32330261 PMCID: PMC7604850 DOI: 10.1093/jtm/taaa061] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/20/2022]
Abstract
INTRODUCTION International travellers contribute to the rapid spread of Zika virus (ZIKV) and its sentinel identification globally. We describe ZIKV infections among international travellers seen at GeoSentinel sites with a focus on ZIKV acquired in the Americas and the Caribbean, describe countries of exposure and traveller characteristics, and assess ZIKV diagnostic testing by site. METHODS Records with an international travel-related diagnosis of confirmed or probable ZIKV from January 2012 through December 2019 reported to GeoSentinel with a recorded illness onset date were included to show reported cases over time. Records from March 2016 through December 2019 with an exposure region of the Americas or the Caribbean were included in the descriptive analysis. A survey was conducted to assess the availability, accessibility and utilization of ZIKV diagnostic tests at GeoSentinel sites. RESULTS GeoSentinel sites reported 525 ZIKV cases from 2012 through 2019. Between 2012 and 2014, eight cases were reported, and all were acquired in Asia or Oceania. After 2014, most cases were acquired in the Americas or the Caribbean, a large decline in ZIKV cases occurred in 2018-19.Between March 2016 and December 2019, 423 patients acquired ZIKV in the Americas or the Caribbean, peak reporting to these regions occurred in 2016 [330 cases (78%)]. The median age was 36 years (range: 3-92); 63% were female. The most frequent region of exposure was the Caribbean (60%). Thirteen travellers were pregnant during or after travel; one had a sexually acquired ZIKV infection. There was one case of fetal anomaly and two travellers with Guillain-Barré syndrome. GeoSentinel sites reported various challenges to diagnose ZIKV effectively. CONCLUSION ZIKV should remain a consideration for travellers returning from areas with risk of ZIKV transmission. Travellers should discuss their travel plans with their healthcare providers to ensure ZIKV prevention measures are taken.
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Affiliation(s)
- Kristina M Angelo
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA
| | - Rhett J Stoney
- Division of Global Migration and Quarantine, Centers for Disease Control and Prevention, 1600 Clifton Rd NE, Atlanta, GA 30329, USA
| | - Gaelle Brun-Cottan
- Department of Medicine, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118, USA
| | - Karin Leder
- School of Public Health and Preventive Medicine, Victorian Infectious Disease Service, Royal Melbourne Hospital, Doherty Institute for Infection and Immunity, Monash University, 300 Grattan St, Parkville 3050, Australia
| | - Martin P Grobusch
- Center for Tropical Medicine and Travel Medicine, Amsterdam University Medical Centers, University of Amsterdam, 1012 WX Amsterdam, The Netherlands
| | - Natasha Hochberg
- Department of Pediatrics, Boston University School of Medicine, 72 E Concord St, Boston, MA 02118, USA
| | - Susan Kuhn
- Department of Pediatrics, Alberta Health Services, 10101 Southport Rd SW, Calgary AB T2W 3N2, Canada
| | - Emmanuel Bottieau
- Department of Clinical Sciences, Institute of Tropical Medicine, Kronenburgstraat 43, 2000 Antwerp, Belgium
| | - Patricia Schlagenhauf
- WHO Collaborating Centre for Travellers' Health, Epidemiology, Biostatistics, and Prevention Institute, University of Zurich, Rämistrasse 71, 8006 Zurich, Switzerland
| | - Lin Chen
- Division of Infectious Diseases and Travel Medicine, Mount Auburn Hospital, Cambridge and Harvard Medical School, 25 Shattuck St, Boston, MA 02115, USA
| | - Noreen A Hynes
- Johns Hopkins University School of Medicine, 733 N Broadway, Baltimore, MD 21205, USA
| | - Cecilia Perret Perez
- School of Medicine, Universidad Catolica de Chile, Av Libertador Bernardo O'Higgins 340, Santiago, Santiago Metropolitan, Chile
| | - Frank P Mockenhaupt
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Tropical Medicine and International Health, Augustenburger Pl. 1, 13353 Berlin, Germany
| | - Israel Molina
- Department of Infectious Diseases, Vall d'Hebron University Hospital, Universitat Autónoma de Barcelona, PROSICS, Campus de la UAB, Plaça Cívica, 08193, Barcelona, Spain
| | - Clara Crespillo-Andújar
- National Referral Unit for Tropical and Travel Medicine, Department of Internal Medicine, University Hospital La Paz-Carlos III, Paseo de la Castellana, 261, 28046 Madrid, Spain
| | - Denis Malvy
- Department for Infectious Diseases and Tropical Medicine, University Hospital Centre of Bordeaux, and Inserm 1219, University of Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Caumes
- Hôpital Pitié-Salpêtrière, 47-83 Boulevard de l'Hôpital, 75013 Paris, France
| | - Pierre Plourde
- University of Manitoba, 66 Chancellors Cir, Winnipeg MB R3T 2N2, Canada
| | - Marc Shaw
- James Cook University, 1 James Cook Dr, Douglas, Townsville 4811, Australia.,Worldwise Travellers' Health Centres, 18 Saint Marks Road, Remuera, Auckland 1050, New Zealand
| | - Anne E McCarthy
- Department of Medicine, Ottawa Hospital, University of Ottawa, 75 Laurier Ave E, Ottawa K1N 6N5, Canada
| | | | - Bradley A Connor
- The New York Center for Travel and Tropical Medicine, Weill Cornell Medical College, 1300 York Ave, New York, NY 10065, USA
| | - Davidson H Hamer
- Department of Global Health, Boston University School of Public Health, 715 Albany St, Boston, MA 02118, USA.,Section of Infectious Diseases, Department of Medicine, Boston Medical Center, One Boston Medical Center Pl, Boston, MA 02118, USA
| | - Annelies Wilder-Smith
- Department of Epidemiology and Global Health, University of Umea, Petrus Laestadius Väg, 901 87, Umeå, Sweden.,Department for Disease Control, London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, UK
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Ramachandran PS, Wilson MR. Metagenomics for neurological infections - expanding our imagination. Nat Rev Neurol 2020; 16:547-556. [PMID: 32661342 PMCID: PMC7356134 DOI: 10.1038/s41582-020-0374-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/11/2022]
Abstract
Over the past two decades, the diagnosis rate for patients with encephalitis has remained poor despite advances in pathogen-specific testing such as PCR and antigen assays. Metagenomic next-generation sequencing (mNGS) of RNA and DNA extracted from cerebrospinal fluid and brain tissue now offers another strategy for diagnosing neurological infections. Given that mNGS simultaneously assays for a wide range of infectious agents in an unbiased manner, it can identify pathogens that were not part of a neurologist’s initial differential diagnosis either because of the rarity of the infection, because the microorganism has not been previously associated with a clinical phenotype or because it is a newly discovered organism. This Review discusses the technical advantages and pitfalls of cerebrospinal fluid mNGS in the context of patients with neuroinflammatory syndromes, including encephalitis, meningitis and myelitis. We also speculate on how mNGS testing potentially fits into current diagnostic testing algorithms given data on mNGS test performance, cost and turnaround time. Finally, the Review highlights future directions for mNGS technology and other hypothesis-free testing methodologies that are in development. This Review discusses the advantages and pitfalls of metagenomic next-generation sequencing (mNGS) in patients with encephalitis, meningitis and myelitis. The authors outline data on mNGS test performance, cost and turnaround time and highlight future directions for mNGS technology. Meningoencephalitis remains a challenging diagnosis owing to the multitude of possible infectious and autoimmune causes. Meningoencephalitis is associated with a high rate of morbidity and mortality and requires prompt diagnosis and treatment. Metagenomic next-generation sequencing (mNGS) is now a clinically validated test for neuroinfectious diseases that can aid clinicians with a timely diagnosis. mNGS can improve the detection of pathogens that were missed by clinicians or on standard direct testing. mNGS does not perform well when indirect tests are required to make the diagnosis (for example, serology), when infections are compartmentalized and for certain low abundance pathogens. The clinical context of the case is required when interpreting the results of mNGS.
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Affiliation(s)
- Prashanth S Ramachandran
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA.,Department of Neurology, University of California, San Francisco, CA, USA
| | - Michael R Wilson
- Weill Institute for Neurosciences, University of California, San Francisco, CA, USA. .,Department of Neurology, University of California, San Francisco, CA, USA.
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Clemente NS, Ramond A, Turchi Martelli CM, Brickley EB. Geographies of risk: Emerging infectious diseases and travel health data. Travel Med Infect Dis 2020; 36:101806. [PMID: 32592905 PMCID: PMC7314681 DOI: 10.1016/j.tmaid.2020.101806] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 11/24/2022]
Affiliation(s)
- Nuria Sanchez Clemente
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK.
| | - Anna Ramond
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | | | - Elizabeth B Brickley
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
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47
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Lemey P, Hong S, Hill V, Baele G, Poletto C, Colizza V, O’Toole Á, McCrone JT, Andersen KG, Worobey M, Nelson MI, Rambaut A, Suchard MA. Accommodating individual travel history, global mobility, and unsampled diversity in phylogeography: a SARS-CoV-2 case study. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.06.22.165464. [PMID: 32596695 PMCID: PMC7315996 DOI: 10.1101/2020.06.22.165464] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Spatiotemporal bias in genome sequence sampling can severely confound phylogeographic inference based on discrete trait ancestral reconstruction. This has impeded our ability to accurately track the emergence and spread of SARS-CoV-2, which is the virus responsible for the COVID-19 pandemic. Despite the availability of staggering numbers of genomes on a global scale, evolutionary reconstructions of SARS-CoV-2 are hindered by the slow accumulation of sequence divergence over its relatively short transmission history. When confronted with these issues, incorporating additional contextual data may critically inform phylodynamic reconstructions. Here, we present a new approach to integrate individual travel history data in Bayesian phylogeographic inference and apply it to the early spread of SARS-CoV-2, while also including global air transportation data. We demonstrate that including travel history data for each SARS-CoV-2 genome yields more realistic reconstructions of virus spread, particularly when travelers from undersampled locations are included to mitigate sampling bias. We further explore the impact of sampling bias by incorporating unsampled sequences from undersampled locations in the analyses. Our reconstructions reinforce specific transmission hypotheses suggested by the inclusion of travel history data, but also suggest alternative routes of virus migration that are plausible within the epidemiological context but are not apparent with current sampling efforts. Although further research is needed to fully examine the performance of our new data integration approaches and to further improve them, they represent multiple new avenues for directly addressing the colossal issue of sample bias in phylogeographic inference.
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Affiliation(s)
- Philippe Lemey
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Samuel Hong
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Verity Hill
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Guy Baele
- KU Leuven Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Clinical and Evolutionary Virology, Leuven, Belgium
| | - Chiara Poletto
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Vittoria Colizza
- INSERM, Sorbonne Université, Institut Pierre Louis d’Epidémiologie et de Santé Publique IPLESP, F75012 Paris, France
| | - Áine O’Toole
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - John T. McCrone
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Kristian G. Andersen
- Department of Immunology and Microbiology, Scripps Research, La Jolla, CA 92037, USA
| | - Michael Worobey
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA
| | - Martha I. Nelson
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Andrew Rambaut
- Centre for Immunology, Infection and Evolution, University of Edinburgh, King’s Buildings, Edinburgh, EH9 3FL, UK
| | - Marc A. Suchard
- Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
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48
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Jing SL, Huo HF, Xiang H. Modeling the Effects of Meteorological Factors and Unreported Cases on Seasonal Influenza Outbreaks in Gansu Province, China. Bull Math Biol 2020; 82:73. [PMID: 32533498 DOI: 10.1007/s11538-020-00747-6] [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] [Received: 09/13/2019] [Accepted: 05/14/2020] [Indexed: 10/24/2022]
Abstract
Influenza usually breaks out seasonally in temperate regions, especially in winter, infection rates and mortality rates of influenza increase significantly, which means that dry air and cold temperatures accelerate the spread of influenza viruses. However, the meteorological factors that lead to seasonal influenza outbreaks and how these meteorological factors play a decisive role in influenza transmission remain unclear. During the epidemic of infectious diseases, the neglect of unreported cases leads to an underestimation of infection rates and basic reproduction number. In this paper, we propose a new non-autonomous periodic differential equation model with meteorological factors including unreported cases. First, the basic reproduction number is obtained and the global asymptotic stability of the disease-free periodic solution is proved. Furthermore, the existence of periodic solutions and the uniformly persistence of the model are demonstrated. Second, the best-fit parameter values in our model are identified by the MCMC algorithm on the basis of the influenza data in Gansu province, China. We also estimate that the basic reproduction number is 1.2288 (95% CI:(1.2287, 1.2289)). Then, to determine the key parameters of the model, uncertainty and sensitivity analysis are explored. Finally, our results show that influenza is more likely to spread in low temperature, low humidity and low precipitation environments. Temperature is a more important factor than relative humidity and precipitation during the influenza epidemic. In addition, our results also show that there are far more unreported cases than reported cases.
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Affiliation(s)
- Shuang-Lin Jing
- Department of Applied Mathematics, Lanzhou University of Technology, Lanzhou, 730050, Gansu, People's Republic of China
| | - Hai-Feng Huo
- Department of Applied Mathematics, Lanzhou University of Technology, Lanzhou, 730050, Gansu, People's Republic of China.
| | - Hong Xiang
- Department of Applied Mathematics, Lanzhou University of Technology, Lanzhou, 730050, Gansu, People's Republic of China
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49
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Eden JS, Rockett R, Carter I, Rahman H, de Ligt J, Hadfield J, Storey M, Ren X, Tulloch R, Basile K, Wells J, Byun R, Gilroy N, O'Sullivan MV, Sintchenko V, Chen SC, Maddocks S, Sorrell TC, Holmes EC, Dwyer DE, Kok J. An emergent clade of SARS-CoV-2 linked to returned travellers from Iran. Virus Evol 2020; 6:veaa027. [PMID: 32296544 PMCID: PMC7147362 DOI: 10.1093/ve/veaa027] [Citation(s) in RCA: 95] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The SARS-CoV-2 epidemic has rapidly spread outside China with major outbreaks occurring in Italy, South Korea, and Iran. Phylogenetic analyses of whole-genome sequencing data identified a distinct SARS-CoV-2 clade linked to travellers returning from Iran to Australia and New Zealand. This study highlights potential viral diversity driving the epidemic in Iran, and underscores the power of rapid genome sequencing and public data sharing to improve the detection and management of emerging infectious diseases.
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Affiliation(s)
- John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia
| | - Rebecca Rockett
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Ian Carter
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Hossinur Rahman
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Joep de Ligt
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - James Hadfield
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Matthew Storey
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - Xiaoyun Ren
- Institute of Environmental Science and Research, Porirua 5240, New Zealand
| | - Rachel Tulloch
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Jessica Wells
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Roy Byun
- NSW Ministry of Health, North Sydney, NSW 2059, Australia
| | - Nicky Gilroy
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Matthew V O'Sullivan
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Vitali Sintchenko
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Sharon C Chen
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Susan Maddocks
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Tania C Sorrell
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Virus Research & Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, PO Box 412, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Dominic E Dwyer
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences & School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia.,Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology - Institute of Clinical Pathology and Medical Research, Westmead, NSW 2145, Australia.,Centre for Infectious Diseases and Microbiology - Public Health, Westmead Hospital, Westmead, NSW 2145, Australia
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50
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Pérez-Losada M, Arenas M, Galán JC, Bracho MA, Hillung J, García-González N, González-Candelas F. High-throughput sequencing (HTS) for the analysis of viral populations. INFECTION GENETICS AND EVOLUTION 2020; 80:104208. [PMID: 32001386 DOI: 10.1016/j.meegid.2020.104208] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/21/2020] [Accepted: 01/24/2020] [Indexed: 12/12/2022]
Abstract
The development of High-Throughput Sequencing (HTS) technologies is having a major impact on the genomic analysis of viral populations. Current HTS platforms can capture nucleic acid variation across millions of genes for both selected amplicons and full viral genomes. HTS has already facilitated the discovery of new viruses, hinted new taxonomic classifications and provided a deeper and broader understanding of their diversity, population and genetic structure. Hence, HTS has already replaced standard Sanger sequencing in basic and applied research fields, but the next step is its implementation as a routine technology for the analysis of viruses in clinical settings. The most likely application of this implementation will be the analysis of viral genomics, because the huge population sizes, high mutation rates and very fast replacement of viral populations have demonstrated the limited information obtained with Sanger technology. In this review, we describe new technologies and provide guidelines for the high-throughput sequencing and genetic and evolutionary analyses of viral populations and metaviromes, including software applications. With the development of new HTS technologies, new and refurbished molecular and bioinformatic tools are also constantly being developed to process and integrate HTS data. These allow assembling viral genomes and inferring viral population diversity and dynamics. Finally, we also present several applications of these approaches to the analysis of viral clinical samples including transmission clusters and outbreak characterization.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Washington, DC, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain; Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain.
| | - Juan Carlos Galán
- Microbiology Service, Hospital Ramón y Cajal, Madrid, Spain; CIBER in Epidemiology and Public Health, Spain.
| | - Mª Alma Bracho
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain.
| | - Julia Hillung
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Neris García-González
- Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
| | - Fernando González-Candelas
- CIBER in Epidemiology and Public Health, Spain; Joint Research Unit "Infection and Public Health" FISABIO-University of Valencia, Valencia, Spain; Institute for Integrative Systems Biology (I2SysBio), CSIC-University of Valencia, Valencia, Spain.
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