1
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Uyeki TM, Milton S, Abdul Hamid C, Reinoso Webb C, Presley SM, Shetty V, Rollo SN, Martinez DL, Rai S, Gonzales ER, Kniss KL, Jang Y, Frederick JC, De La Cruz JA, Liddell J, Di H, Kirby MK, Barnes JR, Davis CT. Highly Pathogenic Avian Influenza A(H5N1) Virus Infection in a Dairy Farm Worker. N Engl J Med 2024. [PMID: 38700506 DOI: 10.1056/nejmc2405371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Affiliation(s)
| | - Scott Milton
- Texas Department of State Health Services, Lubbock, TX
| | | | | | - Steven M Presley
- Texas Tech University Bioterrorism Response Laboratory, Lubbock, TX
| | - Varun Shetty
- Texas Department of State Health Services, Austin, TX
| | - Susan N Rollo
- Texas Department of State Health Services, Austin, TX
| | | | - Saroj Rai
- Texas Department of State Health Services, Austin, TX
| | | | | | - Yunho Jang
- Centers for Disease Control and Prevention, Atlanta, GA
| | | | | | - Jimma Liddell
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Han Di
- Centers for Disease Control and Prevention, Atlanta, GA
| | - Marie K Kirby
- Centers for Disease Control and Prevention, Atlanta, GA
| | - John R Barnes
- Centers for Disease Control and Prevention, Atlanta, GA
| | - C Todd Davis
- Centers for Disease Control and Prevention, Atlanta, GA
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2
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VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MSY, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. PLoS Pathog 2024; 20:e1012131. [PMID: 38626244 PMCID: PMC11051653 DOI: 10.1371/journal.ppat.1012131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 04/26/2024] [Accepted: 03/16/2024] [Indexed: 04/18/2024] Open
Abstract
Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype swine IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intrahost Single Nucleotide Variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
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Affiliation(s)
- David VanInsberghe
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
| | - Dillon S. McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Max S. Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Samuel S. Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, Georgia, United States of America
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR), Atlanta, Georgia, United States of America
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3
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Keller MW, Keong LM, Rambo-Martin BL, Hassell N, Lacek KA, Wilson MM, Kirby MK, Liddell J, Owuor DC, Sheth M, Madden J, Lee JS, Kondor RJ, Wentworth DE, Barnes JR. Targeted amplification and genetic sequencing of the severe acute respiratory syndrome coronavirus 2 surface glycoprotein. Microbiol Spectr 2024; 12:e0298223. [PMID: 38084972 PMCID: PMC10783008 DOI: 10.1128/spectrum.02982-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/09/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE The COVID-19 pandemic was accompanied by an unprecedented surveillance effort. The resulting data were and will continue to be critical for surveillance and control of SARS-CoV-2. However, some genomic surveillance methods experienced challenges as the virus evolved, resulting in incomplete and poor quality data. Complete and quality coverage, especially of the S-gene, is important for supporting the selection of vaccine candidates. As such, we developed a robust method to target the S-gene for amplification and sequencing. By focusing on the S-gene and imposing strict coverage and quality metrics, we hope to increase the quality of surveillance data for this continually evolving gene. Our technique is currently being deployed globally to partner laboratories, and public health representatives from 79 countries have received hands-on training and support. Expanding access to quality surveillance methods will undoubtedly lead to earlier detection of novel variants and better inform vaccine strain selection.
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Affiliation(s)
- Matthew W. Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Lisa M. Keong
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Benjamin L. Rambo-Martin
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Norman Hassell
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Kristine A. Lacek
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Malania M. Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Marie K. Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Jimma Liddell
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - D. Collins Owuor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Mili Sheth
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Joseph Madden
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Justin S. Lee
- Biotechnology Core Facility Branch, Division of Scientific Resources, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rebecca J. Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - David E. Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R. Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Author Correction: Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2024; 30:307. [PMID: 37946059 PMCID: PMC10803257 DOI: 10.1038/s41591-023-02684-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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Shu B, Wilson MM, Keller MW, Tran H, Sokol T, Lee G, Rambo‐Martin BL, Kirby MK, Hassell N, Haydel D, Hand J, Wentworth DE, Barnes JR. In-field detection and characterization of B/Victoria lineage deletion variant viruses causing early influenza activity and an outbreak in Louisiana, 2019. Influenza Other Respir Viruses 2024; 18:e13246. [PMID: 38188372 PMCID: PMC10767671 DOI: 10.1111/irv.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/06/2023] [Accepted: 12/10/2023] [Indexed: 01/09/2024] Open
Abstract
Background In 2019, the Louisiana Department of Health reported an early influenza B/Victoria (B/VIC) virus outbreak. Method As it was an atypically large outbreak, we deployed to Louisiana to investigate it using genomics and a triplex real-time RT-PCR assay to detect three antigenically distinct B/VIC lineage variant viruses. Results The investigation indicated that B/VIC V1A.3 subclade, containing a three amino acid deletion in the hemagglutinin and known to be antigenically distinct to the B/Colorado/06/2017 vaccine virus, was the most prevalent circulating virus within the specimens evaluated (86/88 in real-time RT-PCR). Conclusion This work underscores the value of portable platforms for rapid, onsite pathogen characterization.
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Affiliation(s)
- Bo Shu
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Malania M. Wilson
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Matthew W. Keller
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Ha Tran
- Louisiana Department of HealthOffice of Public Health LaboratoryBaton RougeLouisianaUSA
| | - Theresa Sokol
- Louisiana Department of HealthOffice of Public Health, Infectious Disease EpidemiologyNew OrleansLouisianaUSA
| | - Grace Lee
- Louisiana Department of HealthOffice of Public Health, Infectious Disease EpidemiologyNew OrleansLouisianaUSA
| | - Benjamin L. Rambo‐Martin
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Marie K. Kirby
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Norman Hassell
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - Danielle Haydel
- Louisiana Department of HealthOffice of Public Health LaboratoryBaton RougeLouisianaUSA
| | - Julie Hand
- Louisiana Department of HealthOffice of Public Health, Infectious Disease EpidemiologyNew OrleansLouisianaUSA
| | - David E. Wentworth
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
| | - John R. Barnes
- Virology, Surveillance and Diagnosis Branch, Influenza DivisionCenters for Disease Control and PreventionAtlantaGeorgiaUSA
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6
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Owuor DC, de Laurent ZR, Nyawanda BO, Emukule GO, Kondor R, Barnes JR, Nokes DJ, Agoti CN, Chaves SS. Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons. Sci Rep 2023; 13:22342. [PMID: 38102198 PMCID: PMC10724140 DOI: 10.1038/s41598-023-49157-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 12/05/2023] [Indexed: 12/17/2023] Open
Abstract
Influenza viruses undergo rapid evolutionary changes, which requires continuous surveillance to monitor for genetic and potential antigenic changes in circulating viruses that can guide control and prevention decision making. We sequenced and phylogenetically analyzed A(H1N1)pdm09 virus genome sequences obtained from specimens collected from hospitalized patients of all ages with or without pneumonia between 2009 and 2018 from seven sentinel surveillance sites across Kenya. We compared these sequences with recommended vaccine strains during the study period to infer genetic and potential antigenic changes in circulating viruses and associations of clinical outcome. We generated and analyzed a total of 383 A(H1N1)pdm09 virus genome sequences. Phylogenetic analyses of HA protein revealed that multiple genetic groups (clades, subclades, and subgroups) of A(H1N1)pdm09 virus circulated in Kenya over the study period; these evolved away from their vaccine strain, forming clades 7 and 6, subclades 6C, 6B, and 6B.1, and subgroups 6B.1A and 6B.1A1 through acquisition of additional substitutions. Several amino acid substitutions among circulating viruses were associated with continued evolution of the viruses, especially in antigenic epitopes and receptor binding sites (RBS) of circulating viruses. Disease severity declined with an increase in age among children aged < 5 years. Our study highlights the necessity of timely genomic surveillance to monitor the evolutionary changes of influenza viruses. Routine influenza surveillance with broad geographic representation and whole genome sequencing capacity to inform on prioritization of antigenic analysis and the severity of circulating strains are critical to improved selection of influenza strains for inclusion in vaccines.
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Affiliation(s)
- D Collins Owuor
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya.
| | - Zaydah R de Laurent
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Gideon O Emukule
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
| | - Rebecca Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - D James Nokes
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), University of Warwick, Coventry, UK
| | - Charles N Agoti
- Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Kilifi, Kenya
- School of Public Health and Human Sciences, Pwani University, Kilifi, Kenya
| | - Sandra S Chaves
- Influenza Division, Centers for Disease Control and Prevention, Nairobi, Kenya
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA, USA
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7
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VanInsberghe D, McBride DS, DaSilva J, Stark TJ, Lau MS, Shepard SS, Barnes JR, Bowman AS, Lowen AC, Koelle K. Genetic drift and purifying selection shape within-host influenza A virus populations during natural swine infections. bioRxiv 2023:2023.10.23.563581. [PMID: 37961583 PMCID: PMC10634741 DOI: 10.1101/2023.10.23.563581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Patterns of within-host influenza A virus (IAV) diversity and evolution have been described in natural human infections, but these patterns remain poorly characterized in non-human hosts. Elucidating these dynamics is important to better understand IAV biology and the evolutionary processes that govern spillover into humans. Here, we sampled an IAV outbreak in pigs during a week-long county fair to characterize viral diversity and evolution in this important reservoir host. Nasal wipes were collected on a daily basis from all pigs present at the fair, yielding up to 421 samples per day. Subtyping of PCR-positive samples revealed the co-circulation of H1N1 and H3N2 subtype IAVs. PCR-positive samples with robust Ct values were deep-sequenced, yielding 506 sequenced samples from a total of 253 pigs. Based on higher-depth re-sequenced data from a subset of these initially sequenced samples (260 samples from 168 pigs), we characterized patterns of within-host IAV genetic diversity and evolution. We find that IAV genetic diversity in single-subtype infected pigs is low, with the majority of intra-host single nucleotide variants (iSNVs) present at frequencies of <10%. The ratio of the number of nonsynonymous to the number of synonymous iSNVs is significantly lower than under the neutral expectation, indicating that purifying selection shapes patterns of within-host viral diversity in swine. The dynamic turnover of iSNVs and their pronounced frequency changes further indicate that genetic drift also plays an important role in shaping IAV populations within pigs. Taken together, our results highlight similarities in patterns of IAV genetic diversity and evolution between humans and swine, including the role of stochastic processes in shaping within-host IAV dynamics.
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Affiliation(s)
- David VanInsberghe
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, 30322
- Department of Biology, Emory University, Atlanta, GA, 30322
| | - Dillon S. McBride
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Max S.Y. Lau
- Department of Biostatistics and Bioinformatics, Rollins School of Public Health, Emory University, Atlanta, GA, 30322
| | - Samuel S. Shepard
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA
| | - Andrew S. Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH 43210
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University, Atlanta, GA, 30322
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR)
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA, 30322
- Emory Center of Excellence for Influenza Research and Response (Emory-CEIRR)
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8
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Perofsky AC, Huddleston J, Hansen C, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Lewis N, Whittaker L, Ermetal B, Harvey R, Galiano M, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Sullivan SG, Barr IG, Subbarao K, Krammer F, Bedford T, Viboud C. Antigenic drift and subtype interference shape A(H3N2) epidemic dynamics in the United States. medRxiv 2023:2023.10.02.23296453. [PMID: 37873362 PMCID: PMC10593063 DOI: 10.1101/2023.10.02.23296453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Influenza viruses continually evolve new antigenic variants, through mutations in epitopes of their major surface proteins, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift potentiates the reinfection of previously infected individuals, but the contribution of this process to variability in annual epidemics is not well understood. Here we link influenza A(H3N2) virus evolution to regional epidemic dynamics in the United States during 1997-2019. We integrate phenotypic measures of HA antigenic drift and sequence-based measures of HA and NA fitness to infer antigenic and genetic distances between viruses circulating in successive seasons. We estimate the magnitude, severity, timing, transmission rate, age-specific patterns, and subtype dominance of each regional outbreak and find that genetic distance based on broad sets of epitope sites is the strongest evolutionary predictor of A(H3N2) virus epidemiology. Increased HA and NA epitope distance between seasons correlates with larger, more intense epidemics, higher transmission, greater A(H3N2) subtype dominance, and a greater proportion of cases in adults relative to children, consistent with increased population susceptibility. Based on random forest models, A(H1N1) incidence impacts A(H3N2) epidemics to a greater extent than viral evolution, suggesting that subtype interference is a major driver of influenza A virus infection dynamics, presumably via heterosubtypic cross-immunity.
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Affiliation(s)
- Amanda C Perofsky
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
| | - Chelsea Hansen
- Fogarty International Center, National Institutes of Health, United States
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), United States
| | - Nicola Lewis
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Ruth Harvey
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Monica Galiano
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick Institute, United Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious Diseases, Japan
| | - Sheena G Sullivan
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Ian G Barr
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Kanta Subbarao
- WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Australia
| | - Florian Krammer
- Center for Vaccine Research and Pandemic Preparedness (C-VaRPP), Icahn School of Medicine at Mount Sinai, United States
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, United States
| | - Trevor Bedford
- Brotman Baty Institute for Precision Medicine, University of Washington, United States
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Center, United States
- Department of Genome Sciences, University of Washington, United States
- Howard Hughes Medical Institute, Seattle, United States
| | - Cécile Viboud
- Fogarty International Center, National Institutes of Health, United States
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9
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Kieran TJ, DaSilva J, Stark TJ, York IA, Pappas C, Barnes JR, Maines TR, Belser JA. Influenza A Virus Multicycle Replication Yields Comparable Viral Population Emergence in Human Respiratory and Ocular Cell Types. Microbiol Spectr 2023; 11:e0116623. [PMID: 37404140 PMCID: PMC10433845 DOI: 10.1128/spectrum.01166-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/06/2023] Open
Abstract
While primarily considered a respiratory pathogen, influenza A virus (IAV) is nonetheless capable of spreading to, and replicating in, numerous extrapulmonary tissues in humans. However, within-host assessments of genetic diversity during multicycle replication have been largely limited to respiratory tract tissues and specimens. As selective pressures can vary greatly between anatomical sites, there is a need to examine how measures of viral diversity may vary between influenza viruses exhibiting different tropisms in humans, as well as following influenza virus infection of cells derived from different organ systems. Here, we employed human primary tissue constructs emulative of the human airway or corneal surface, and we infected both with a panel of human- and avian-origin IAV, inclusive of H1 and H3 subtype human viruses and highly pathogenic H5 and H7 subtype viruses, which are associated with both respiratory disease and conjunctivitis following human infection. While both cell types supported productive replication of all viruses, airway-derived tissue constructs elicited greater induction of genes associated with antiviral responses than did corneal-derived constructs. We used next-generation sequencing to examine viral mutations and population diversity, utilizing several metrics. With few exceptions, generally comparable measures of viral diversity and mutational frequency were detected following homologous virus infection of both respiratory-origin and ocular-origin tissue constructs. Expansion of within-host assessments of genetic diversity to include IAV with atypical clinical presentations in humans or in extrapulmonary cell types can provide greater insight into understanding those features most prone to modulation in the context of viral tropism. IMPORTANCE Influenza A virus (IAV) can infect tissues both within and beyond the respiratory tract, leading to extrapulmonary complications, such as conjunctivitis or gastrointestinal disease. Selective pressures governing virus replication and induction of host responses can vary based on the anatomical site of infection, yet studies examining within-host assessments of genetic diversity are typically only conducted in cells derived from the respiratory tract. We examined the contribution of influenza virus tropism on these properties two different ways: by using IAV associated with different tropisms in humans, and by infecting human cell types from two different organ systems susceptible to IAV infection. Despite the diversity of cell types and viruses employed, we observed generally similar measures of viral diversity postinfection across all conditions tested; these findings nonetheless contribute to a greater understanding of the role tissue type contributes to the dynamics of virus evolution within a human host.
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Affiliation(s)
- Troy J. Kieran
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Juliana DaSilva
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Thomas J. Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Ian A. York
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Claudia Pappas
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R. Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Taronna R. Maines
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jessica A. Belser
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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10
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Kniss K, Sumner KM, Tastad KJ, Lewis NM, Jansen L, Julian D, Reh M, Carlson E, Williams R, Koirala S, Buss B, Donahue M, Palm J, Kollmann L, Holzbauer S, Levine MZ, Davis T, Barnes JR, Flannery B, Brammer L, Fry A. Risk for Infection in Humans after Exposure to Birds Infected with Highly Pathogenic Avian Influenza A(H5N1) Virus, United States, 2022. Emerg Infect Dis 2023; 29:1215-1219. [PMID: 37095080 DOI: 10.3201/eid2906.230103] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023] Open
Abstract
During February 7─September 3, 2022, a total of 39 states experienced outbreaks of highly pathogenic avian influenza A(H5N1) virus in birds from commercial poultry farms and backyard flocks. Among persons exposed to infected birds, highly pathogenic avian influenza A(H5) viral RNA was detected in 1 respiratory specimen from 1 person.
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11
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Lacek KA, Rambo-Martin BL, Batra D, Zheng XY, Hassell N, Sakaguchi H, Peacock T, Groves N, Keller M, Wilson MM, Sheth M, Davis ML, Borroughs M, Gerhart J, Shepard SS, Cook PW, Lee J, Wentworth DE, Barnes JR, Kondor R, Paden CR. SARS-CoV-2 Delta-Omicron Recombinant Viruses, United States. Emerg Infect Dis 2022; 28:1442-1445. [PMID: 35551714 PMCID: PMC9239886 DOI: 10.3201/eid2807.220526] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta-Omicron recombinant genomes from Centers for Disease Control and Prevention national genomic surveillance. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta-Omicron spike protein.
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12
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Welch NL, Zhu M, Hua C, Weller J, Mirhashemi ME, Nguyen TG, Mantena S, Bauer MR, Shaw BM, Ackerman CM, Thakku SG, Tse MW, Kehe J, Uwera MM, Eversley JS, Bielwaski DA, McGrath G, Braidt J, Johnson J, Cerrato F, Moreno GK, Krasilnikova LA, Petros BA, Gionet GL, King E, Huard RC, Jalbert SK, Cleary ML, Fitzgerald NA, Gabriel SB, Gallagher GR, Smole SC, Madoff LC, Brown CM, Keller MW, Wilson MM, Kirby MK, Barnes JR, Park DJ, Siddle KJ, Happi CT, Hung DT, Springer M, MacInnis BL, Lemieux JE, Rosenberg E, Branda JA, Blainey PC, Sabeti PC, Myhrvold C. Multiplexed CRISPR-based microfluidic platform for clinical testing of respiratory viruses and identification of SARS-CoV-2 variants. Nat Med 2022; 28:1083-1094. [PMID: 35130561 PMCID: PMC9117129 DOI: 10.1038/s41591-022-01734-1] [Citation(s) in RCA: 97] [Impact Index Per Article: 48.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/03/2022] [Indexed: 11/23/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.
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Affiliation(s)
- Nicole L Welch
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Harvard Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA.
| | - Meilin Zhu
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Catherine Hua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Juliane Weller
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - Tien G Nguyen
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | - Matthew R Bauer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Bennett M Shaw
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Cheri M Ackerman
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sri Gowtham Thakku
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Megan W Tse
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jared Kehe
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Jacqueline S Eversley
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Derek A Bielwaski
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Graham McGrath
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Joseph Braidt
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | | | | | - Gage K Moreno
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Lydia A Krasilnikova
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Brittany A Petros
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and Massachusetts Institute of Technology, Cambridge, MA, USA
- Harvard/Massachusetts Institute of Technology MD-PhD Program, Harvard Medical School, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Ewa King
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | - Richard C Huard
- State Health Laboratories, Rhode Island Department of Health, Providence, RI, USA
| | | | - Michael L Cleary
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | | | | | - Sandra C Smole
- Massachusetts Department of Public Health, Boston, MA, USA
| | | | | | - Matthew W Keller
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Marie K Kirby
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel J Park
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katherine J Siddle
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Christian T Happi
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- African Centre of Excellence for Genomics of Infectious Diseases, Redeemer's University, Ede, Nigeria
- Department of Biological Sciences, College of Natural Sciences, Redeemer's University, Ede, Nigeria
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Michael Springer
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Bronwyn L MacInnis
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Jacob E Lemieux
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Eric Rosenberg
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - John A Branda
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Pardis C Sabeti
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA.
- Koch Institute for Integrative Cancer Research at Massachusetts Institute of Technology, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - Cameron Myhrvold
- Department of Molecular Biology, Princeton University, Princeton, NJ, USA.
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13
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Chung JR, Kim SS, Kondor RJ, Smith C, Budd AP, Tartof SY, Florea A, Talbot HK, Grijalva CG, Wernli KJ, Phillips CH, Monto AS, Martin ET, Belongia EA, McLean HQ, Gaglani M, Reis M, Geffel KM, Nowalk MP, DaSilva J, Keong LM, Stark TJ, Barnes JR, Wentworth DE, Brammer L, Burns E, Fry AM, Patel MM, Flannery B. Interim Estimates of 2021-22 Seasonal Influenza Vaccine Effectiveness - United States, February 2022. MMWR Morb Mortal Wkly Rep 2022; 71:365-370. [PMID: 35271561 PMCID: PMC8911998 DOI: 10.15585/mmwr.mm7110a1] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
In the United States, annual vaccination against seasonal influenza is recommended for all persons aged ≥6 months except when contraindicated (1). Currently available influenza vaccines are designed to protect against four influenza viruses: A(H1N1)pdm09 (the 2009 pandemic virus), A(H3N2), B/Victoria lineage, and B/Yamagata lineage. Most influenza viruses detected this season have been A(H3N2) (2). With the exception of the 2020-21 season, when data were insufficient to generate an estimate, CDC has estimated the effectiveness of seasonal influenza vaccine at preventing laboratory-confirmed, mild/moderate (outpatient) medically attended acute respiratory infection (ARI) each season since 2004-05. This interim report uses data from 3,636 children and adults with ARI enrolled in the U.S. Influenza Vaccine Effectiveness Network during October 4, 2021-February 12, 2022. Overall, vaccine effectiveness (VE) against medically attended outpatient ARI associated with influenza A(H3N2) virus was 16% (95% CI = -16% to 39%), which is considered not statistically significant. This analysis indicates that influenza vaccination did not reduce the risk for outpatient medically attended illness with influenza A(H3N2) viruses that predominated so far this season. Enrollment was insufficient to generate reliable VE estimates by age group or by type of influenza vaccine product (1). CDC recommends influenza antiviral medications as an adjunct to vaccination; the potential public health benefit of antiviral medications is magnified in the context of reduced influenza VE. CDC routinely recommends that health care providers continue to administer influenza vaccine to persons aged ≥6 months as long as influenza viruses are circulating, even when VE against one virus is reduced, because vaccine can prevent serious outcomes (e.g., hospitalization, intensive care unit (ICU) admission, or death) that are associated with influenza A(H3N2) virus infection and might protect against other influenza viruses that could circulate later in the season.
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14
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Olson SM, Newhams MM, Halasa NB, Feldstein LR, Novak T, Weiss SL, Coates BM, Schuster JE, Schwarz AJ, Maddux AB, Hall MW, Nofziger RA, Flori HR, Gertz SJ, Kong M, Sanders RC, Irby K, Hume JR, Cullimore ML, Shein SL, Thomas NJ, Stewart LS, Barnes JR, Patel MM, Randolph AG. Vaccine Effectiveness Against Life-Threatening Influenza Illness in US Children. Clin Infect Dis 2022; 75:230-238. [PMID: 35024795 DOI: 10.1093/cid/ciab931] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Predominance of 2 antigenically drifted influenza viruses during the 2019-2020 season offered an opportunity to assess vaccine effectiveness against life-threatening pediatric influenza disease from vaccine-mismatched viruses in the United States. METHODS We enrolled children aged <18 years admitted to the intensive care unit with acute respiratory infection across 17 hospitals. Respiratory specimens were tested using reverse-transcription polymerase chain reaction for influenza viruses and sequenced. Using a test-negative design, we estimated vaccine effectiveness comparing odds of vaccination in test-positive case patients vs test-negative controls, stratifying by age, virus type, and severity. Life-threating influenza included death or invasive mechanical ventilation, vasopressors, cardiopulmonary resuscitation, dialysis, or extracorporeal membrane oxygenation. RESULTS We enrolled 159 critically ill influenza case-patients (70% ≤8 years; 51% A/H1N1pdm09 and 25% B-Victoria viruses) and 132 controls (69% were aged ≤8 years). Among 56 sequenced A/H1N1pdm09 viruses, 29 (52%) were vaccine-mismatched (A/H1N1pdm09/5A+156K) and 23 (41%) were vaccine-matched (A/H1N1pdm09/5A+187A,189E). Among sequenced B-lineage viruses, majority (30 of 31) were vaccine-mismatched. Effectiveness against critical influenza was 63% (95% confidence interval [CI], 38% to 78%) and similar by age. Effectiveness was 75% (95% CI, 49% to 88%) against life-threatening influenza vs 57% (95% CI, 24% to 76%) against non-life-threating influenza. Effectiveness was 78% (95% CI, 41% to 92%) against matched A(H1N1)pdm09 viruses, 47% (95% CI, -21% to 77%) against mismatched A(H1N1)pdm09 viruses, and 75% (95% CI, 37% to 90%) against mismatched B-Victoria viruses. CONCLUSIONS During a season when vaccine-mismatched influenza viruses predominated, vaccination was associated with a reduced risk of critical and life-threatening influenza illness in children.
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Affiliation(s)
- Samantha M Olson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M Newhams
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Natasha B Halasa
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Leora R Feldstein
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Tanya Novak
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, USA
| | - Scott L Weiss
- Division of Critical Care, Department of Anesthesiology and Critical Care, The University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Bria M Coates
- Division of Critical Care Medicine, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, Illinois, USA
| | - Jennifer E Schuster
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Children's Mercy Kansas City, Kansas City, Missouri, USA
| | - Adam J Schwarz
- Department of Pediatrics, Children's Hospital of Orange County, Orange, California, USA
| | - Aline B Maddux
- Department of Pediatrics, Section of Critical Care Medicine, University of Colorado School of Medicine and Children's Hospital Colorado, Aurora, Colorado, USA
| | - Mark W Hall
- Division of Critical Care Medicine, Department of Pediatrics, Nationwide Children's Hospital, Columbus, Ohio, USA
| | - Ryan A Nofziger
- Division of Critical Care Medicine, Department of Pediatrics, Akron Children's Hospital, Akron, Ohio, USA
| | - Heidi R Flori
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, Mott Children's Hospital and University of Michigan, Ann Arbor, Michigan, USA
| | - Shira J Gertz
- Division of Pediatric Critical Care, Department of Pediatrics, Saint Barnabas Medical Center, Livingston, New Jersey, USA
| | - Michele Kong
- Division of Pediatric Critical Care Medicine, Department of Pediatrics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ronald C Sanders
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Katherine Irby
- Section of Pediatric Critical Care, Department of Pediatrics, Arkansas Children's Hospital, Little Rock, Arkansas, USA
| | - Janet R Hume
- Division of Pediatric Critical Care, University of Minnesota Masonic Children's Hospital, Minneapolis, Minnesota, USA
| | - Melissa L Cullimore
- Division of Pediatric Critical Care, Department of Pediatrics, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Steven L Shein
- Division of Pediatric Critical Care Medicine, Rainbow Babies and Children's Hospital, Cleveland, Ohio, USA
| | - Neal J Thomas
- Department of Pediatrics, Penn State Hershey Children's Hospital, Penn State University College of Medicine, Hershey, Pennsylvania, USA
| | - Laura S Stewart
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish M Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Adrienne G Randolph
- Department of Anesthesiology, Critical Care and Pain Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.,Department of Anesthesia, Harvard Medical School, Boston, Massachusetts, USA.,Department of Pediatrics, Harvard Medical School, Boston, Massachusetts, USA
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15
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Tenforde MW, Kondor RJG, Chung JR, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Belongia EA, McLean HQ, Gaglani M, Rao A, Kim SS, Stark TJ, Barnes JR, Wentworth DE, Patel MM, Flannery B. Effect of Antigenic Drift on Influenza Vaccine Effectiveness in the United States-2019-2020. Clin Infect Dis 2021; 73:e4244-e4250. [PMID: 33367650 PMCID: PMC8664438 DOI: 10.1093/cid/ciaa1884] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND At the start of the 2019-2020 influenza season, concern arose that circulating B/Victoria viruses of the globally emerging clade V1A.3 were antigenically drifted from the strain included in the vaccine. Intense B/Victoria activity was followed by circulation of genetically diverse A(H1N1)pdm09 viruses that were also antigenically drifted. We measured vaccine effectiveness (VE) in the United States against illness from these emerging viruses. METHODS We enrolled outpatients aged ≥6 months with acute respiratory illness at 5 sites. Respiratory specimens were tested for influenza by reverse-transcriptase polymerase chain reaction (RT-PCR). Using the test-negative design, we determined influenza VE by virus subtype/lineage and genetic subclades by comparing odds of vaccination in influenza cases versus test-negative controls. RESULTS Among 8845 enrollees, 2722 (31%) tested positive for influenza, including 1209 (44%) for B/Victoria and 1405 (51%) for A(H1N1)pdm09. Effectiveness against any influenza illness was 39% (95% confidence interval [CI]: 32-44), 45% (95% CI: 37-52) against B/Victoria and 30% (95% CI: 21-39) against A(H1N1)pdm09-associated illness. Vaccination offered no protection against A(H1N1)pdm09 viruses with antigenically drifted clade 6B.1A 183P-5A+156K HA genes (VE 7%; 95% CI: -14 to 23%) which predominated after January. CONCLUSIONS Vaccination provided protection against influenza illness, mainly due to infections from B/Victoria viruses. Vaccine protection against illness from A(H1N1)pdm09 was lower than historically observed effectiveness of 40%-60%, due to late-season vaccine mismatch following emergence of antigenically drifted viruses. The effect of drift on vaccine protection is not easy to predict and, even in drifted years, significant protection can be observed.
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Affiliation(s)
| | | | - Jessie R Chung
- Centers for Disease Control and Prevention, Atlanta GA, USA
| | | | | | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle WA, USA
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle WA, USA
| | | | | | | | - Huong Q McLean
- Marshfield Clinic Research Institute, Marshfield WI, USA
| | - Manjusha Gaglani
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple TX, USA
| | - Arundhati Rao
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple TX, USA
| | - Sara S Kim
- Centers for Disease Control and Prevention, Atlanta GA, USA
| | - Thomas J Stark
- Centers for Disease Control and Prevention, Atlanta GA, USA
| | - John R Barnes
- Centers for Disease Control and Prevention, Atlanta GA, USA
| | | | - Manish M Patel
- Centers for Disease Control and Prevention, Atlanta GA, USA
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16
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Owuor DC, de Laurent ZR, Kikwai GK, Mayieka LM, Ochieng M, Müller NF, Otieno NA, Emukule GO, Hunsperger EA, Garten R, Barnes JR, Chaves SS, Nokes DJ, Agoti CN. Characterizing the Countrywide Epidemic Spread of Influenza A(H1N1)pdm09 Virus in Kenya between 2009 and 2018. Viruses 2021; 13:1956. [PMID: 34696386 PMCID: PMC8539974 DOI: 10.3390/v13101956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/13/2021] [Accepted: 09/22/2021] [Indexed: 12/01/2022] Open
Abstract
The spatiotemporal patterns of spread of influenza A(H1N1)pdm09 viruses on a countrywide scale are unclear in many tropical/subtropical regions mainly because spatiotemporally representative sequence data are lacking. We isolated, sequenced, and analyzed 383 A(H1N1)pdm09 viral genomes from hospitalized patients between 2009 and 2018 from seven locations across Kenya. Using these genomes and contemporaneously sampled global sequences, we characterized the spread of the virus in Kenya over several seasons using phylodynamic methods. The transmission dynamics of A(H1N1)pdm09 virus in Kenya were characterized by (i) multiple virus introductions into Kenya over the study period, although only a few of those introductions instigated local seasonal epidemics that then established local transmission clusters, (ii) persistence of transmission clusters over several epidemic seasons across the country, (iii) seasonal fluctuations in effective reproduction number (Re) associated with lower number of infections and seasonal fluctuations in relative genetic diversity after an initial rapid increase during the early pandemic phase, which broadly corresponded to epidemic peaks in the northern and southern hemispheres, (iv) high virus genetic diversity with greater frequency of seasonal fluctuations in 2009-2011 and 2018 and low virus genetic diversity with relatively weaker seasonal fluctuations in 2012-2017, and (v) virus spread across Kenya. Considerable influenza virus diversity circulated within Kenya, including persistent viral lineages that were unique to the country, which may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied low-to-middle-income tropical and subtropical regions is required to understand the full diversity and global ecology of influenza viruses in humans and to inform vaccination strategies within these regions.
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Affiliation(s)
- D. Collins Owuor
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Zaydah R. de Laurent
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
| | - Gilbert K. Kikwai
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Lillian M. Mayieka
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Melvin Ochieng
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Nicola F. Müller
- Fred Hutchinson Cancer Research Center, Vaccine and Infectious Disease Division, Seattle, WA 98109, USA;
| | - Nancy A. Otieno
- Kenya Medical Research Institute (KEMRI), Nairobi 54840-00200, Kenya; (G.K.K.); (L.M.M.); (M.O.); (N.A.O.)
| | - Gideon O. Emukule
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
| | - Elizabeth A. Hunsperger
- Centers for Disease Control and Prevention, Division of Global Health Protection, Nairobi 606-00621, Kenya;
- Centers for Disease Control and Prevention, Division of Global Health Protection, Atlanta, GA 30333, USA
| | - Rebecca Garten
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - John R. Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - Sandra S. Chaves
- Centers for Disease Control and Prevention (CDC), Influenza Division, Nairobi 606-00621, Kenya; (G.O.E.); (S.S.C.)
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention, Atlanta, GA 30333, USA; (R.G.); (J.R.B.)
| | - D. James Nokes
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Life Sciences and Zeeman Institute for Systems Biology and Infectious Disease Epidemiology Research (SBIDER), Coventry CV4 7AL, UK
| | - Charles N. Agoti
- Wellcome Trust Research Programme, Epidemiology and Demography Department, Kenya Medical Research Institute (KEMRI), Kilifi 230-80108, Kenya; (Z.R.d.L.); (D.J.N.); (C.N.A.)
- School of Public Health and Human Sciences, Pwani University, Kilifi 195-80108, Kenya
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17
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Tenforde MW, Talbot HK, Trabue CH, Gaglani M, McNeal TM, Monto AS, Martin ET, Zimmerman RK, Silveira FP, Middleton DB, Olson SM, Garten Kondor RJ, Barnes JR, Ferdinands JM, Patel MM. Influenza Vaccine Effectiveness Against Hospitalization in the United States, 2019-2020. J Infect Dis 2021; 224:813-820. [PMID: 33378531 PMCID: PMC8408767 DOI: 10.1093/infdis/jiaa800] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 12/23/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Influenza causes significant morbidity and mortality and stresses hospital resources during periods of increased circulation. We evaluated the effectiveness of the 2019-2020 influenza vaccine against influenza-associated hospitalization in the United States. METHODS We included adults hospitalized with acute respiratory illness at 14 hospitals and tested for influenza viruses by reserve-transcription polymerase chain reaction. Vaccine effectiveness (VE) was estimated by comparing the odds of current-season influenza vaccination in test-positive influenza cases vs test-negative controls, adjusting for confounders. VE was stratified by age and major circulating influenza types along with A(H1N1)pdm09 genetic subgroups. RESULTS A total of 3116 participants were included, including 18% (n = 553) influenza-positive cases. Median age was 63 years. Sixty-seven percent (n = 2079) received vaccination. Overall adjusted VE against influenza viruses was 41% (95% confidence interval [CI], 27%-52%). VE against A(H1N1)pdm09 viruses was 40% (95% CI, 24%-53%) and 33% against B viruses (95% CI, 0-56%). Of the 2 major A(H1N1)pdm09 subgroups (representing 90% of sequenced H1N1 viruses), VE against one group (5A + 187A,189E) was 59% (95% CI, 34%-75%) whereas no VE was observed against the other group (5A + 156K) (-1% [95% CI, -61% to 37%]). CONCLUSIONS In a primarily older population, influenza vaccination was associated with a 41% reduction in risk of hospitalized influenza illness.
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Affiliation(s)
- Mark W Tenforde
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - H Keipp Talbot
- Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Christopher H Trabue
- University of Tennessee Health Science Center, Saint Thomas Health, Nashville, Tennessee, USA
| | - Manjusha Gaglani
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Tresa M McNeal
- Baylor Scott and White Health, Texas A&M University College of Medicine, Temple, Texas, USA
| | - Arnold S Monto
- University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, Michigan, USA
| | - Richard K Zimmerman
- University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Fernanda P Silveira
- University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Donald B Middleton
- University of Pittsburgh School of Medicine and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Samantha M Olson
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Rebecca J Garten Kondor
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jill M Ferdinands
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Manish M Patel
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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18
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Schrodt CA, Malenfant JH, Hunter JC, Slifka KJ, Campbell A, Stone N, Whitehouse ER, Wittry B, Christensen B, Barnes JR, Brammer L, Hemarajata P, Green NM, Civen R, Gounder PP, Rao AK. Investigation of a Suspect Severe Acute Respiratory Syndrome Coronavirus-2 and Influenza A Mixed Outbreak: Lessons Learned for Long-Term Care Facilities Nationwide. Clin Infect Dis 2021; 73:S77-S80. [PMID: 33956136 PMCID: PMC8135935 DOI: 10.1093/cid/ciab372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A suspected outbreak of influenza A and SARS-CoV-2 at a long-term care facility in Los Angeles County was months later, determined to not involve influenza. To prevent inadvertent transmission of infections, facilities should use highly specific influenza diagnostics and follow CDC guidelines that specifically address infection control challenges.
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Affiliation(s)
- Caroline A Schrodt
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | - Jason H Malenfant
- Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Jennifer C Hunter
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Kara Jacobs Slifka
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Angela Campbell
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Nimalie Stone
- Division of Healthcare Quality Promotion, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Erin R Whitehouse
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA.,CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | - Beth Wittry
- CDC COVID-19 Response Team, Atlanta, Georgia, USA
| | | | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lynnette Brammer
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Peera Hemarajata
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey, California, USA
| | - Nicole M Green
- Public Health Laboratory, Los Angeles County Department of Public Health, Downey, California, USA
| | - Rachel Civen
- Community Health Services Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Prabhu P Gounder
- Acute Communicable Disease Control Program, Los Angeles County Department of Public Health, Los Angeles, California, USA
| | - Agam K Rao
- CDC COVID-19 Response Team, Atlanta, Georgia, USA
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19
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Shu B, Kirby MK, Davis WG, Warnes C, Liddell J, Liu J, Wu KH, Hassell N, Benitez AJ, Wilson MM, Keller MW, Rambo-Martin BL, Camara Y, Winter J, Kondor RJ, Zhou B, Spies S, Rose LE, Winchell JM, Limbago BM, Wentworth DE, Barnes JR. Multiplex Real-Time Reverse Transcription PCR for Influenza A Virus, Influenza B Virus, and Severe Acute Respiratory Syndrome Coronavirus 2. Emerg Infect Dis 2021; 27:1821-1830. [PMID: 34152951 PMCID: PMC8237866 DOI: 10.3201/eid2707.210462] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 102.0, influenza B virus at 102.2, and SARS-CoV-2 at 100.3 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2.
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20
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Ganti K, Bagga A, DaSilva J, Shepard SS, Barnes JR, Shriner S, Koelle K, Lowen AC. Avian Influenza A Viruses Reassort and Diversify Differently in Mallards and Mammals. Viruses 2021; 13:v13030509. [PMID: 33808674 PMCID: PMC8003500 DOI: 10.3390/v13030509] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 03/10/2021] [Accepted: 03/16/2021] [Indexed: 12/18/2022] Open
Abstract
Reassortment among co-infecting influenza A viruses (IAVs) is an important source of viral diversity and can facilitate expansion into novel host species. Indeed, reassortment played a key role in the evolution of the last three pandemic IAVs. Observed patterns of reassortment within a coinfected host are likely to be shaped by several factors, including viral load, the extent of viral mixing within the host and the stringency of selection. These factors in turn are expected to vary among the diverse host species that IAV infects. To investigate host differences in IAV reassortment, here we examined reassortment of two distinct avian IAVs within their natural host (mallards) and a mammalian model system (guinea pigs). Animals were co-inoculated with A/wildbird/California/187718-36/2008 (H3N8) and A/mallard/Colorado/P66F1-5/2008 (H4N6) viruses. Longitudinal samples were collected from the cloaca of mallards or the nasal tract of guinea pigs and viral genetic exchange was monitored by genotyping clonal isolates from these samples. Relative to those in guinea pigs, viral populations in mallards showed higher frequencies of reassortant genotypes and were characterized by higher genotype richness and diversity. In line with these observations, analysis of pairwise segment combinations revealed lower linkage disequilibrium in mallards as compared to guinea pigs. No clear longitudinal patterns in richness, diversity or linkage disequilibrium were present in either host. Our results reveal mallards to be a highly permissive host for IAV reassortment and suggest that reduced viral mixing limits avian IAV reassortment in a mammalian host.
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Affiliation(s)
- Ketaki Ganti
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Anish Bagga
- Emory College of Arts and Sciences, Emory University, Atlanta, GA 30322, USA;
| | - Juliana DaSilva
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - Samuel S. Shepard
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - John R. Barnes
- Center for Disease Control and Prevention, Influenza Division, Atlanta, GA 30322, USA; (J.D.); (S.S.S.); (J.R.B.)
| | - Susan Shriner
- National Wildlife Research Center, US Department of Agriculture-Animal and Plant Health Inspection Service, Fort Collins, CO 80521, USA;
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA 30322, USA
- Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA
- Correspondence: (K.K.); , (A.C.L.)
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA 30322, USA;
- Emory-UGA Center of Excellence for Influenza Research and Surveillance (CEIRS), Atlanta, GA 30322, USA
- Correspondence: (K.K.); , (A.C.L.)
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21
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Zhou B, Thao TTN, Hoffmann D, Taddeo A, Ebert N, Labroussaa F, Pohlmann A, King J, Steiner S, Kelly JN, Portmann J, Halwe NJ, Ulrich L, Trüeb BS, Fan X, Hoffmann B, Wang L, Thomann L, Lin X, Stalder H, Pozzi B, de Brot S, Jiang N, Cui D, Hossain J, Wilson MM, Keller MW, Stark TJ, Barnes JR, Dijkman R, Jores J, Benarafa C, Wentworth DE, Thiel V, Beer M. SARS-CoV-2 spike D614G change enhances replication and transmission. Nature 2021; 592:122-127. [PMID: 33636719 DOI: 10.1038/s41586-021-03361-1] [Citation(s) in RCA: 334] [Impact Index Per Article: 111.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/16/2021] [Indexed: 12/18/2022]
Abstract
During the evolution of SARS-CoV-2 in humans, a D614G substitution in the spike glycoprotein (S) has emerged; virus containing this substitution has become the predominant circulating variant in the COVID-19 pandemic1. However, whether the increasing prevalence of this variant reflects a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains unknown. Here we use isogenic SARS-CoV-2 variants to demonstrate that the variant that contains S(D614G) has enhanced binding to the human cell-surface receptor angiotensin-converting enzyme 2 (ACE2), increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a human ACE2 knock-in mouse model, and markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Our data show that the D614G substitution in S results in subtle increases in binding and replication in vitro, and provides a real competitive advantage in vivo-particularly during the transmission bottleneck. Our data therefore provide an explanation for the global predominance of the variant that contains S(D614G) among the SARS-CoV-2 viruses that are currently circulating.
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Affiliation(s)
- Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Adriano Taddeo
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Jenna N Kelly
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Bettina Salome Trüeb
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xiaoyu Fan
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Li Wang
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lisa Thomann
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xudong Lin
- Battelle Memorial Institute, Atlanta, GA, USA
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Berta Pozzi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Nannan Jiang
- Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA
| | - Dan Cui
- Battelle Memorial Institute, Atlanta, GA, USA
| | - Jaber Hossain
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Malania M Wilson
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Matthew W Keller
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Thomas J Stark
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barnes
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland.,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.,Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Charaf Benarafa
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - David E Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Mittelhäusern, Switzerland. .,Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany.
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22
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Shu B, Kirby MK, Warnes C, Sessions WM, Davis WG, Liu J, Wilson MM, Lindstrom S, Wentworth DE, Barnes JR. Detection and discrimination of influenza B Victoria lineage deletion variant viruses by real-time RT-PCR. ACTA ACUST UNITED AC 2021; 25. [PMID: 33063654 PMCID: PMC7565853 DOI: 10.2807/1560-7917.es.2020.25.41.1900652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Background During the 2016/17 influenza season, influenza B/VIC lineage variant viruses emerged with two (K162N163) or three (K162N163D164) amino acid (aa) deletions in the haemagglutinin (HA) protein. There are currently five antigenically distinct HA proteins expressed by co-circulating influenza B viruses: B/YAM, B/VIC V1A (no deletion), B/VIC V1A-2DEL (2 aa deletion) and two antigenically distinguishable groups of B/VIC V1A-3DEL (3 aa deletion). The prevalence of these viruses differs across geographical regions, making it critical to have a sensitive, rapid diagnostic assay that detects and distinguishes these influenza B variant viruses during surveillance. Aim Our objective was to develop a real-time RT-PCR (rRT-PCR) assay for detection and discrimination of influenza B/VIC lineage variant viruses. Methods We designed a diagnostic assay with one pair of conserved primers and three probes specific to each genetic group. We used propagated influenza B/VIC variant viruses and clinical specimens to assess assay performance. Results This rRT-PCR assay detects and distinguishes the influenza B/VIC V1A, B/VIC V1A-2DEL, and B/VIC V1A-3DEL variant viruses, with no cross-reactivity. This assay can be run as a multiplex reaction, allowing for increased testing efficiency and reduced cost. Conclusion Coupling this assay with the Centers for Disease Control and Prevention’s Human Influenza Virus Real-Time RT-PCR Diagnostic Panel Influenza B Lineage Genotyping Kit results in rapid detection and characterisation of circulating influenza B viruses. Detailed surveillance information on these distinct influenza B variant viruses will provide insight into their prevalence and geographical distribution and could aid in vaccine recommendations.
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Affiliation(s)
- Bo Shu
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Marie K Kirby
- Battelle Memorial Institute, Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Christine Warnes
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Wendy M Sessions
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - William G Davis
- Battelle Memorial Institute, Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Ji Liu
- Chickasaw Nation Industries, Inc., Atlanta, United States.,Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Malania M Wilson
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - Stephen Lindstrom
- Respiratory Virus Branch, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, United States
| | - David E Wentworth
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
| | - John R Barnes
- Virology, Surveillance and Diagnostic Branch, Influenza Division, Centers for Disease Control and Prevention, Atlanta, United States
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23
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Zhou B, Thao TTN, Hoffmann D, Taddeo A, Ebert N, Labroussaa F, Pohlmann A, King J, Portmann J, Halwe NJ, Ulrich L, Trüeb BS, Kelly JN, Fan X, Hoffmann B, Steiner S, Wang L, Thomann L, Lin X, Stalder H, Pozzi B, de Brot S, Jiang N, Cui D, Hossain J, Wilson M, Keller M, Stark TJ, Barnes JR, Dijkman R, Jores J, Benarafa C, Wentworth DE, Thiel V, Beer M. SARS-CoV-2 spike D614G variant confers enhanced replication and transmissibility. bioRxiv 2020:2020.10.27.357558. [PMID: 33140052 PMCID: PMC7605563 DOI: 10.1101/2020.10.27.357558] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic 1 . However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro , it provides a real competitive advantage in vivo , particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.
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Affiliation(s)
- Bin Zhou
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Tran Thi Nhu Thao
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Donata Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Adriano Taddeo
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nadine Ebert
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Fabien Labroussaa
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Anne Pohlmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jacqueline King
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Jasmine Portmann
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nico Joel Halwe
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Lorenz Ulrich
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Bettina Salome Trüeb
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jenna N. Kelly
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xiaoyu Fan
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Bernd Hoffmann
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Silvio Steiner
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Biomedical Science, University of Bern, Bern, Switzerland
| | - Li Wang
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Lisa Thomann
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Xudong Lin
- Battelle Memorial Institute, Atlanta, Georgia, United States of America
| | - Hanspeter Stalder
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Berta Pozzi
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Simone de Brot
- COMPATH, Institute of Animal Pathology, University of Bern, Bern, Switzerland
| | - Nannan Jiang
- Oak Ridge Institute for Science and Education, Oak Ridge, Tennessee, United States of America
| | - Dan Cui
- Battelle Memorial Institute, Atlanta, Georgia, United States of America
| | - Jaber Hossain
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Malania Wilson
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Matthew Keller
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Thomas J. Stark
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - John R. Barnes
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ronald Dijkman
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Joerg Jores
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Institute of Veterinary Bacteriology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Charaf Benarafa
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - David E. Wentworth
- CDC COVID-19 Response, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Volker Thiel
- Institute of Virology and Immunology (IVI), Bern and Mittelhäusern, Switzerland
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
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24
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Huddleston J, Barnes JR, Rowe T, Xu X, Kondor R, Wentworth DE, Whittaker L, Ermetal B, Daniels RS, McCauley JW, Fujisaki S, Nakamura K, Kishida N, Watanabe S, Hasegawa H, Barr I, Subbarao K, Barrat-Charlaix P, Neher RA, Bedford T. Integrating genotypes and phenotypes improves long-term forecasts of seasonal influenza A/H3N2 evolution. eLife 2020; 9:e60067. [PMID: 32876050 PMCID: PMC7553778 DOI: 10.7554/elife.60067] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/24/2020] [Indexed: 12/17/2022] Open
Abstract
Seasonal influenza virus A/H3N2 is a major cause of death globally. Vaccination remains the most effective preventative. Rapid mutation of hemagglutinin allows viruses to escape adaptive immunity. This antigenic drift necessitates regular vaccine updates. Effective vaccine strains need to represent H3N2 populations circulating one year after strain selection. Experts select strains based on experimental measurements of antigenic drift and predictions made by models from hemagglutinin sequences. We developed a novel influenza forecasting framework that integrates phenotypic measures of antigenic drift and functional constraint with previously published sequence-only fitness estimates. Forecasts informed by phenotypic measures of antigenic drift consistently outperformed previous sequence-only estimates, while sequence-only estimates of functional constraint surpassed more comprehensive experimentally-informed estimates. Importantly, the best models integrated estimates of both functional constraint and either antigenic drift phenotypes or recent population growth.
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Affiliation(s)
- John Huddleston
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
- Molecular and Cell Biology Program, University of WashingtonSeattleUnited States
| | - John R Barnes
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC)AtlantaUnited States
| | - Thomas Rowe
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC)AtlantaUnited States
| | - Xiyan Xu
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC)AtlantaUnited States
| | - Rebecca Kondor
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC)AtlantaUnited States
| | - David E Wentworth
- Virology Surveillance and Diagnosis Branch, Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC)AtlantaUnited States
| | - Lynne Whittaker
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick InstituteLondonUnited Kingdom
| | - Burcu Ermetal
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick InstituteLondonUnited Kingdom
| | - Rodney Stuart Daniels
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick InstituteLondonUnited Kingdom
| | - John W McCauley
- WHO Collaborating Centre for Reference and Research on Influenza, Crick Worldwide Influenza Centre, The Francis Crick InstituteLondonUnited Kingdom
| | - Seiichiro Fujisaki
- Influenza Virus Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Kazuya Nakamura
- Influenza Virus Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Noriko Kishida
- Influenza Virus Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Shinji Watanabe
- Influenza Virus Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Hideki Hasegawa
- Influenza Virus Research Center, National Institute of Infectious DiseasesTokyoJapan
| | - Ian Barr
- The WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Kanta Subbarao
- The WHO Collaborating Centre for Reference and Research on Influenza, The Peter Doherty Institute for Infection and Immunity, Department of Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - Pierre Barrat-Charlaix
- Biozentrum, University of BaselBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Richard A Neher
- Biozentrum, University of BaselBaselSwitzerland
- Swiss Institute of BioinformaticsBaselSwitzerland
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
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25
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Jeffers SV, Dreizler S, Barnes JR, Haswell CA, Nelson RP, Rodríguez E, López-González MJ, Morales N, Luque R, Zechmeister M, Vogt SS, Jenkins JS, Palle E, Berdi Ñas ZM, Coleman GAL, Díaz MR, Ribas I, Jones HRA, Butler RP, Tinney CG, Bailey J, Carter BD, O'Toole S, Wittenmyer RA, Crane JD, Feng F, Shectman SA, Teske J, Reiners A, Amado PJ, Anglada-Escudé G. A multiplanet system of super-Earths orbiting the brightest red dwarf star GJ 887. Science 2020; 368:1477-1481. [PMID: 32587019 DOI: 10.1126/science.aaz0795] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 05/12/2020] [Indexed: 11/02/2022]
Abstract
The closet exoplanets to the Sun provide opportunities for detailed characterization of planets outside the Solar System. We report the discovery, using radial velocity measurements, of a compact multiplanet system of super-Earth exoplanets orbiting the nearby red dwarf star GJ 887. The two planets have orbital periods of 9.3 and 21.8 days. Assuming an Earth-like albedo, the equilibrium temperature of the 21.8-day planet is ~350 kelvin. The planets are interior to, but close to the inner edge of, the liquid-water habitable zone. We also detect an unconfirmed signal with a period of ~50 days, which could correspond to a third super-Earth in a more temperate orbit. Our observations show that GJ 887 has photometric variability below 500 parts per million, which is unusually quiet for a red dwarf.
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Affiliation(s)
- S V Jeffers
- Institut für Astrophysik, Georg-August-UniversitÄt, 37077 Göttingen, Germany.
| | - S Dreizler
- Institut für Astrophysik, Georg-August-UniversitÄt, 37077 Göttingen, Germany
| | - J R Barnes
- School of Physical Sciences, The Open University, Milton Keynes MK7 6AA, UK
| | - C A Haswell
- School of Physical Sciences, The Open University, Milton Keynes MK7 6AA, UK
| | - R P Nelson
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK
| | - E Rodríguez
- Instituto de Astrofísica de Andalucía, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - M J López-González
- Instituto de Astrofísica de Andalucía, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - N Morales
- Instituto de Astrofísica de Andalucía, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - R Luque
- Instituto de Astrofísica de Canarias, 38205 La Laguna, Tenerife, Spain.,Departamento de Astrofísica, Universidad de La Laguna, 38206 La Laguna, Tenerife, Spain
| | - M Zechmeister
- Institut für Astrophysik, Georg-August-UniversitÄt, 37077 Göttingen, Germany
| | - S S Vogt
- University of California/Lick Observatory, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - J S Jenkins
- Departamento de Astronomia, Universidad de Chile, Santiago, Chile.,Centro de Astrofísica y Tecnologías Afines, Santiago, Chile
| | - E Palle
- Instituto de Astrofísica de Canarias, 38205 La Laguna, Tenerife, Spain.,Departamento de Astrofísica, Universidad de La Laguna, 38206 La Laguna, Tenerife, Spain
| | - Z M Berdi Ñas
- Departamento de Astronomia, Universidad de Chile, Santiago, Chile
| | - G A L Coleman
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK.,Physikalisches Institut, UniversitÄt Bern, 3012 Bern, Switzerland
| | - M R Díaz
- Departamento de Astronomia, Universidad de Chile, Santiago, Chile
| | - I Ribas
- Institut de Ciències de l'Espai, Consejo Superior de Investigaciones Científicas, Campus Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.,Istitut d'Estudis Espacials de Catalunya, E-08034 Barcelona, Spain
| | - H R A Jones
- Centre for Astrophysics Research, University of Hertfordshire, Hatfield AL10 9AB, UK
| | - R P Butler
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - C G Tinney
- Exoplanetary Science at University of New South Wales, School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
| | - J Bailey
- Exoplanetary Science at University of New South Wales, School of Physics, University of New South Wales, Sydney, NSW 2052, Australia
| | - B D Carter
- Centre for Astrophysics, University of Southern Queensland, Springfield Central, QLD 4300, Australia
| | - S O'Toole
- Australian Astronomical Optics, Macquarie University, North Ryde, NSW 2113, Australia
| | - R A Wittenmyer
- Centre for Astrophysics, University of Southern Queensland, Toowoomba, QLD 4350, Australia
| | - J D Crane
- The Observatories of the Carnegie Institution for Science, Pasadena, CA 91101, USA
| | - F Feng
- Earth and Planets Laboratory, Carnegie Institution for Science, Washington, DC 20015, USA
| | - S A Shectman
- The Observatories of the Carnegie Institution for Science, Pasadena, CA 91101, USA
| | - J Teske
- The Observatories of the Carnegie Institution for Science, Pasadena, CA 91101, USA
| | - A Reiners
- Institut für Astrophysik, Georg-August-UniversitÄt, 37077 Göttingen, Germany
| | - P J Amado
- Instituto de Astrofísica de Andalucía, Consejo Superior de Investigaciones Científicas, 18008 Granada, Spain
| | - G Anglada-Escudé
- School of Physics and Astronomy, Queen Mary University of London, London E1 4NS, UK.,Institut de Ciències de l'Espai, Consejo Superior de Investigaciones Científicas, Campus Universitat Autònoma de Barcelona, E-08193 Bellaterra, Spain.,Istitut d'Estudis Espacials de Catalunya, E-08034 Barcelona, Spain
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26
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Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TSF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC. Massively multiplexed nucleic acid detection with Cas13. Nature 2020; 582:277-282. [PMID: 32349121 PMCID: PMC7332423 DOI: 10.1038/s41586-020-2279-8] [Citation(s) in RCA: 379] [Impact Index Per Article: 94.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 04/20/2020] [Indexed: 12/26/2022]
Abstract
The great majority of globally circulating pathogens go undetected, undermining patient care and hindering outbreak preparedness and response. To enable routine surveillance and comprehensive diagnostic applications, there is a need for detection technologies that can scale to test many samples1-3 while simultaneously testing for many pathogens4-6. Here, we develop Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN), a platform for scalable, multiplexed pathogen detection. In the CARMEN platform, nanolitre droplets containing CRISPR-based nucleic acid detection reagents7 self-organize in a microwell array8 to pair with droplets of amplified samples, testing each sample against each CRISPR RNA (crRNA) in replicate. The combination of CARMEN and Cas13 detection (CARMEN-Cas13) enables robust testing of more than 4,500 crRNA-target pairs on a single array. Using CARMEN-Cas13, we developed a multiplexed assay that simultaneously differentiates all 169 human-associated viruses with at least 10 published genome sequences and rapidly incorporated an additional crRNA to detect the causative agent of the 2020 COVID-19 pandemic. CARMEN-Cas13 further enables comprehensive subtyping of influenza A strains and multiplexed identification of dozens of HIV drug-resistance mutations. The intrinsic multiplexing and throughput capabilities of CARMEN make it practical to scale, as miniaturization decreases reagent cost per test by more than 300-fold. Scalable, highly multiplexed CRISPR-based nucleic acid detection shifts diagnostic and surveillance efforts from targeted testing of high-priority samples to comprehensive testing of large sample sets, greatly benefiting patients and public health9-11.
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Affiliation(s)
- Cheri M Ackerman
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Cameron Myhrvold
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA.
| | - Sri Gowtham Thakku
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Catherine A Freije
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Ph.D. Program in Virology, Division of Medical Sciences, Harvard Medical School, Boston, MA, USA
| | - Hayden C Metsky
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Electrical Engineering and Computer Science, MIT, Cambridge, MA, USA
| | - David K Yang
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Simon H Ye
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Division of Health Sciences and Technology, Harvard Medical School and MIT, Cambridge, MA, USA
| | - Chloe K Boehm
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | | | - Jared Kehe
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - Tien G Nguyen
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Amber Carter
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
| | - Anthony Kulesa
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Biological Engineering, MIT, Cambridge, MA, USA
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Vivien G Dugan
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Deborah T Hung
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Molecular Biology Department and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Paul C Blainey
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA.
- Department of Biological Engineering, MIT, Cambridge, MA, USA.
- Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA, USA.
| | - Pardis C Sabeti
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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27
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Dawood FS, Chung JR, Kim SS, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Belongia EA, McLean HQ, Gaglani M, Dunnigan K, Foust A, Sessions W, DaSilva J, Le S, Stark T, Kondor RJ, Barnes JR, Wentworth DE, Brammer L, Fry AM, Patel MM, Flannery B. Interim Estimates of 2019-20 Seasonal Influenza Vaccine Effectiveness - United States, February 2020. MMWR Morb Mortal Wkly Rep 2020; 69:177-182. [PMID: 32078591 PMCID: PMC7043386 DOI: 10.15585/mmwr.mm6907a1] [Citation(s) in RCA: 92] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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28
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Rambo-Martin BL, Keller MW, Wilson MM, Nolting JM, Anderson TK, Vincent AL, Bagal UR, Jang Y, Neuhaus EB, Davis CT, Bowman AS, Wentworth DE, Barnes JR. Influenza A Virus Field Surveillance at a Swine-Human Interface. mSphere 2020; 5:e00822-19. [PMID: 32024713 PMCID: PMC7002310 DOI: 10.1128/msphere.00822-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 01/07/2020] [Indexed: 12/20/2022] Open
Abstract
While working overnight at a swine exhibition, we identified an influenza A virus (IAV) outbreak in swine, Nanopore sequenced 13 IAV genomes from samples we collected, and predicted in real time that these viruses posed a novel risk to humans due to genetic mismatches between the viruses and current prepandemic candidate vaccine viruses (CVVs). We developed and used a portable IAV sequencing and analysis platform called Mia (Mobile Influenza Analysis) to complete and characterize full-length consensus genomes approximately 18 h after unpacking the mobile lab. Exhibition swine are a known source for zoonotic transmission of IAV to humans and pose a potential pandemic risk. Genomic analyses of IAV in swine are critical to understanding this risk, the types of viruses circulating in swine, and whether current vaccines developed for use in humans would be predicted to provide immune protection. Nanopore sequencing technology has enabled genome sequencing in the field at the source of viral outbreaks or at the bedside or pen-side of infected humans and animals. The acquired data, however, have not yet demonstrated real-time, actionable public health responses. The Mia system rapidly identified three genetically distinct swine IAV lineages from three subtypes, A(H1N1), A(H3N2), and A(H1N2). Analysis of the hemagglutinin (HA) sequences of the A(H1N2) viruses identified >30 amino acid differences between the HA1 of these viruses and the most closely related CVV. As an exercise in pandemic preparedness, all sequences were emailed to CDC collaborators who initiated the development of a synthetically derived CVV.IMPORTANCE Swine are influenza virus reservoirs that have caused outbreaks and pandemics. Genomic characterization of these viruses enables pandemic risk assessment and vaccine comparisons, though this typically occurs after a novel swine virus jumps into humans. The greatest risk occurs where large groups of swine and humans comingle. At a large swine exhibition, we used Nanopore sequencing and on-site analytics to interpret 13 swine influenza virus genomes and identified an influenza virus cluster that was genetically highly varied to currently available vaccines. As part of the National Strategy for Pandemic Preparedness exercises, the sequences were emailed to colleagues at the CDC who initiated the development of a synthetically derived vaccine designed to match the viruses at the exhibition. Subsequently, this virus caused 14 infections in humans and was the dominant U.S. variant virus in 2018.
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Affiliation(s)
| | - Matthew W Keller
- Oak Ridge Institute of Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | - Malania M Wilson
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Jacqueline M Nolting
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Tavis K Anderson
- National Animal Disease Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | - Amy L Vincent
- National Animal Disease Center, Agricultural Research Service (ARS), U.S. Department of Agriculture (USDA), Ames, Iowa, USA
| | | | - Yunho Jang
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Elizabeth B Neuhaus
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - C Todd Davis
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Andrew S Bowman
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
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Flannery B, Kondor RJG, Chung JR, Gaglani M, Reis M, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Belongia EA, McLean HQ, Kim SS, Blanton L, Kniss K, Budd AP, Brammer L, Stark TJ, Barnes JR, Wentworth DE, Fry AM, Patel M. Spread of Antigenically Drifted Influenza A(H3N2) Viruses and Vaccine Effectiveness in the United States During the 2018-2019 Season. J Infect Dis 2020; 221:8-15. [PMID: 31665373 PMCID: PMC7325528 DOI: 10.1093/infdis/jiz543] [Citation(s) in RCA: 118] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Increased illness due to antigenically drifted A(H3N2) clade 3C.3a influenza viruses prompted concerns about vaccine effectiveness (VE) and vaccine strain selection. We used US virologic surveillance and US Influenza Vaccine Effectiveness (Flu VE) Network data to evaluate consequences of this clade. METHODS Distribution of influenza viruses was described using virologic surveillance data. The Flu VE Network enrolled ambulatory care patients aged ≥6 months with acute respiratory illness at 5 sites. Respiratory specimens were tested for influenza by means of reverse-transcriptase polymerase chain reaction and were sequenced. Using a test-negative design, we estimated VE, comparing the odds of influenza among vaccinated versus unvaccinated participants. RESULTS During the 2018-2019 influenza season, A(H3N2) clade 3C.3a viruses caused an increasing proportion of influenza cases. Among 2763 Flu VE Network case patients, 1325 (48%) were infected with A(H1N1)pdm09 and 1350 (49%) with A(H3N2); clade 3C.3a accounted for 977 (93%) of 1054 sequenced A(H3N2) viruses. VE was 44% (95% confidence interval, 37%-51%) against A(H1N1)pdm09 and 9% (-4% to 20%) against A(H3N2); VE was 5% (-10% to 19%) against A(H3N2) clade 3C.3a viruses. CONCLUSIONS The predominance of A(H3N2) clade 3C.3a viruses during the latter part of the 2018-2019 season was associated with decreased VE, supporting the A(H3N2) vaccine component update for 2019-2020 northern hemisphere influenza vaccines.
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Affiliation(s)
- Brendan Flannery
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Jessie R Chung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Manjusha Gaglani
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas
| | - Michael Reis
- Baylor Scott & White Health, Texas A&M University College of Medicine, Temple, Texas
| | - Richard K Zimmerman
- University of Pittsburgh Schools of Health Sciences and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Mary Patricia Nowalk
- University of Pittsburgh Schools of Health Sciences and University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Michael L Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Lisa A Jackson
- Kaiser Permanente Washington Health Research Institute, Seattle, Washington
| | - Arnold S Monto
- University of Michigan School of Public Health, Ann Arbor, Michigan
| | - Emily T Martin
- University of Michigan School of Public Health, Ann Arbor, Michigan
| | | | - Huong Q McLean
- Marshfield Clinic Research Institute, Marshfield, Wisconsin
| | - Sara S Kim
- Oak Ridge Institute for Science and Education Fellowship Program, Oak Ridge, Tennessee
| | - Lenee Blanton
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Krista Kniss
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia P Budd
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lynnette Brammer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas J Stark
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Manish Patel
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
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Almayahi ZK, Al Kindi H, Davies CT, Al-Rawahi B, Al-Jardani A, Al-Yaqoubi F, Jang Y, Jones J, Barnes JR, Davis W, Bo S, Lynch B, Wentworth DE, Al-Maskari Z, Maani AA, Al-Abri S. First report of human infection with avian influenza A(H9N2) virus in Oman: The need for a One Health approach. Int J Infect Dis 2019; 91:169-173. [PMID: 31765821 DOI: 10.1016/j.ijid.2019.11.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 11/18/2019] [Indexed: 10/25/2022] Open
Abstract
Following the detection of the first human case of avian influenza A subtype H9N2 in 1998, more than 40 cases were diagnosed worldwide. However, the spread of the virus has been more remarkable and significant in global poultry populations, causing notable economic losses despite its low pathogenicity. Many surveillance studies and activities conducted in several countries have shown the predominance of this virus subtype. We present the case of a 14-month-old female in Oman with an A(H9N2) virus infection. This is the first human case of A(H9N2) reported from Oman and the Gulf Cooperation Countries, and Oman is the second country outside of southern and eastern Asia to report a case (cases have also been detected in Egypt). The patient had bronchial asthma and presented with a high-grade temperature and symptoms of lower respiratory tract infection that necessitated admission to a high dependency unit in a tertiary care hospital. It is of urgency that a multisector One Health approach be established to combat the threat of avian influenza at the animal-human interface. In addition to enhancements of surveillance and control in poultry, there is a need to develop screening and preventive programs for high-risk occupations.
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Affiliation(s)
- Zayid K Almayahi
- Directorate General for Health Services in South Batinah Governorate, MoH, Rustaq, Oman.
| | - Hanan Al Kindi
- Central Public Health Laboratories, Directorate General for Disease Surveillance and Control, MoH, Oman.
| | - C Todd Davies
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Bader Al-Rawahi
- Directorate General for Disease Surveillance and Control, MoH, Muscat, Oman.
| | - Amina Al-Jardani
- Central Public Health Laboratories, Directorate General for Disease Surveillance and Control, MoH, Oman.
| | - Fatma Al-Yaqoubi
- Directorate General for Disease Surveillance and Control, MoH, Muscat, Oman.
| | - Yunho Jang
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Joyce Jones
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - John R Barnes
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - William Davis
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Shu Bo
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Brian Lynch
- Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | | | | | - Amal Al Maani
- Directorate General for Disease Surveillance and Control, MoH, Muscat, Oman.
| | - Seif Al-Abri
- Directorate General for Disease Surveillance and Control, MoH, Muscat, Oman.
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Yang G, Chowdury S, Hodges E, Rahman MZ, Jang Y, Hossain ME, Jones J, Stark TJ, Di H, Cook PW, Ghosh S, Azziz-Baumgartner E, Barnes JR, Wentworth DE, Kennedy E, Davis CT. Detection of highly pathogenic avian influenza A(H5N6) viruses in waterfowl in Bangladesh. Virology 2019; 534:36-44. [DOI: 10.1016/j.virol.2019.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/21/2019] [Accepted: 05/21/2019] [Indexed: 11/24/2022]
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Doyle JD, Chung JR, Kim SS, Gaglani M, Raiyani C, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Belongia EA, McLean HQ, Foust A, Sessions W, Berman L, Garten RJ, Barnes JR, Wentworth DE, Fry AM, Patel MM, Flannery B. Interim Estimates of 2018-19 Seasonal Influenza Vaccine Effectiveness - United States, February 2019. MMWR Morb Mortal Wkly Rep 2019; 68:135-139. [PMID: 30763298 PMCID: PMC6375657 DOI: 10.15585/mmwr.mm6806a2] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In the United States, annual vaccination against seasonal influenza is recommended for all persons aged ≥6 months (https://www.cdc.gov/flu/protect/whoshouldvax.htm). Effectiveness of seasonal influenza vaccine varies by season. During each influenza season since 2004-05, CDC has estimated the effectiveness of seasonal influenza vaccine to prevent laboratory-confirmed influenza associated with medically attended acute respiratory illness (ARI). This interim report uses data from 3,254 children and adults enrolled in the U.S. Influenza Vaccine Effectiveness Network (U.S. Flu VE Network) during November 23, 2018-February 2, 2019. During this period, overall adjusted vaccine effectiveness against all influenza virus infection associated with medically attended ARI was 47% (95% confidence interval [CI] = 34%-57%). For children aged 6 months-17 years, overall vaccine effectiveness was 61% (44%-73%). Seventy-four percent of influenza A infections for which subtype information was available were caused by A(H1N1)pdm09 viruses. Vaccine effectiveness was estimated to be 46% (30%-58%) against illness caused by influenza A(H1N1)pdm09 viruses. CDC recommends that health care providers continue to administer influenza vaccine because influenza activity is ongoing and the vaccine can still prevent illness, hospitalization, and death associated with currently circulating influenza viruses, or other influenza viruses that might circulate later in the season. During the 2017-18 influenza season, in which influenza A(H3N2) predominated, vaccination was estimated to prevent 7.1 million illnesses, 3.7 million medical visits, 109,000 hospitalizations, and 8,000 deaths (1). Vaccination can also reduce the severity of influenza-associated illness (2). Persons aged ≥6 months who have not yet been vaccinated this season should be vaccinated.
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Keller MW, Rambo-Martin BL, Wilson MM, Ridenour CA, Shepard SS, Stark TJ, Neuhaus EB, Dugan VG, Wentworth DE, Barnes JR. Direct RNA Sequencing of the Coding Complete Influenza A Virus Genome. Sci Rep 2018; 8:14408. [PMID: 30258076 PMCID: PMC6158192 DOI: 10.1038/s41598-018-32615-8] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 09/05/2018] [Indexed: 12/01/2022] Open
Abstract
For the first time, a coding complete genome of an RNA virus has been sequenced in its original form. Previously, RNA was sequenced by the chemical degradation of radiolabeled RNA, a difficult method that produced only short sequences. Instead, RNA has usually been sequenced indirectly by copying it into cDNA, which is often amplified to dsDNA by PCR and subsequently analyzed using a variety of DNA sequencing methods. We designed an adapter to short highly conserved termini of the influenza A virus genome to target the (-) sense RNA into a protein nanopore on the Oxford Nanopore MinION sequencing platform. Utilizing this method with total RNA extracted from the allantoic fluid of influenza rA/Puerto Rico/8/1934 (H1N1) virus infected chicken eggs (EID50 6.8 × 109), we demonstrate successful sequencing of the coding complete influenza A virus genome with 100% nucleotide coverage, 99% consensus identity, and 99% of reads mapped to influenza A virus. By utilizing the same methodology one can redesign the adapter in order to expand the targets to include viral mRNA and (+) sense cRNA, which are essential to the viral life cycle, or other pathogens. This approach also has the potential to identify and quantify splice variants and base modifications, which are not practically measurable with current methods.
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Affiliation(s)
- Matthew W Keller
- Oak Ridge Institute of Science and Education (ORISE), Oak Ridge, Tennessee, USA
| | | | | | | | - Samuel S Shepard
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Thomas J Stark
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Elizabeth B Neuhaus
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - Vivien G Dugan
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - David E Wentworth
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA
| | - John R Barnes
- Influenza Division, National Center for Immunization and Respiratory Diseases (NCIRD), Centers for Disease Control and Prevention (CDC), Atlanta, Georgia, USA.
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Rolfes MA, Millman AJ, Talley P, Elbadawi LI, Kramer NA, Barnes JR, Blanton L, Davis JP, Cole S, Dreisig JJ, Garten R, Haupt T, Jackson MA, Kocharian A, Leifer D, Lynfield R, Martin K, McHugh L, Robinson S, Turabelidze G, Webber LA, Pearce Weinberg M, Wentworth DE, Finelli L, Jhung MA. Influenza-Associated Parotitis During the 2014-2015 Influenza Season in the United States. Clin Infect Dis 2018; 67:485-492. [PMID: 29617957 PMCID: PMC6295667 DOI: 10.1093/cid/ciy136] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 02/13/2018] [Indexed: 02/06/2023] Open
Abstract
Background During the 2014-2015 influenza season in the United States, 256 cases of influenza-associated parotitis were reported from 27 states. We conducted a case-control study and laboratory investigation to further describe this rare clinical manifestation of influenza. Methods During February 2015-April 2015, we interviewed 50 cases (with parotitis) and 124 ill controls (without parotitis) with laboratory-confirmed influenza; participants resided in 11 states and were matched by age, state, hospital admission status, and specimen collection date. Influenza viruses were characterized using real-time polymerase chain reaction and next-generation sequencing. We compared cases and controls using conditional logistic regression. Specimens from additional reported cases were also analyzed. Results Cases, 73% of whom were aged <20 years, experienced painful (86%), unilateral (68%) parotitis a median of 4 (range, 0-16) days after onset of systemic or respiratory symptoms. Cases were more likely than controls to be male (76% vs 51%; P = .005). We detected influenza A(H3N2) viruses, genetic group 3C.2a, in 100% (32/32) of case and 92% (105/108) of control specimens sequenced (P = .22). Influenza B and A(H3N2) 3C.3 and 3C.3b genetic group virus infections were detected in specimens from additional cases. Conclusions Influenza-associated parotitis, as reported here and in prior sporadic case reports, seems to occur primarily with influenza A(H3N2) virus infection. Because of the different clinical and infection control considerations for mumps and influenza virus infections, we recommend clinicians consider influenza in the differential diagnoses among patients with acute parotitis during the influenza season.
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Affiliation(s)
- Melissa A Rolfes
- Epidemic Intelligence Service, Atlanta, Georgia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alexander J Millman
- Epidemic Intelligence Service, Atlanta, Georgia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Pamela Talley
- Epidemic Intelligence Service, Atlanta, Georgia
- Minnesota Department of Health, St. Paul, Madison
| | - Lina I Elbadawi
- Epidemic Intelligence Service, Atlanta, Georgia
- Bureau of Communicable Disease, Wisconsin Division of Public Health, Madison
| | - Natalie A Kramer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lenee Blanton
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jeffrey P Davis
- Bureau of Communicable Disease, Wisconsin Division of Public Health, Madison
| | - Stefanie Cole
- Michigan Department of Health and Human Services, Lansing
| | - John J Dreisig
- New Hampshire Division of Public Health Services, Concord
| | - Rebecca Garten
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas Haupt
- Bureau of Communicable Disease, Wisconsin Division of Public Health, Madison
| | | | - Anna Kocharian
- Bureau of Communicable Disease, Wisconsin Division of Public Health, Madison
| | - Daniel Leifer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Karen Martin
- Minnesota Department of Health, St. Paul, Madison
| | - Lisa McHugh
- Communicable Disease Service, New Jersey Department of Health, Trenton
| | - Sara Robinson
- Maine Center for Disease Control and Prevention, Maine Department of Health and Human Services, Augusta
| | | | - Lori A Webber
- Maine Center for Disease Control and Prevention, Maine Department of Health and Human Services, Augusta
| | - Meghan Pearce Weinberg
- Epidemic Intelligence Service, Atlanta, Georgia
- Michigan Department of Health and Human Services, Lansing
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lyn Finelli
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael A Jhung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
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Elbadawi LI, Talley P, Rolfes MA, Millman AJ, Reisdorf E, Kramer NA, Barnes JR, Blanton L, Christensen J, Cole S, Danz T, Dreisig JJ, Garten R, Haupt T, Isaac BM, Jackson MA, Kocharian A, Leifer D, Martin K, McHugh L, McNall RJ, Palm J, Radford KW, Robinson S, Rosen JB, Sakthivel SK, Shult P, Strain AK, Turabelidze G, Webber LA, Weinberg MP, Wentworth DE, Whitaker BL, Finelli L, Jhung MA, Lynfield R, Davis JP. Non-mumps Viral Parotitis During the 2014-2015 Influenza Season in the United States. Clin Infect Dis 2018; 67:493-501. [PMID: 29617951 PMCID: PMC6240917 DOI: 10.1093/cid/ciy137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 02/13/2018] [Indexed: 12/17/2022] Open
Abstract
Background During the 2014-2015 US influenza season, 320 cases of non-mumps parotitis (NMP) among residents of 21 states were reported to the Centers for Disease Control and Prevention (CDC). We conducted an epidemiologic and laboratory investigation to determine viral etiologies and clinical features of NMP during this unusually large occurrence. Methods NMP was defined as acute parotitis or other salivary gland swelling of >2 days duration in a person with a mumps- negative laboratory result. Using a standardized questionnaire, we collected demographic and clinical information. Buccal samples were tested at the CDC for selected viruses, including mumps, influenza, human parainfluenza viruses (HPIVs) 1-4, adenoviruses, cytomegalovirus, Epstein-Barr virus (EBV), herpes simplex viruses (HSVs) 1 and 2, and human herpes viruses (HHVs) 6A and 6B. Results Among the 320 patients, 65% were male, median age was 14.5 years (range, 0-90), and 67% reported unilateral parotitis. Commonly reported symptoms included sore throat (55%) and fever (48%). Viruses were detected in 210 (71%) of 294 NMP patients with adequate samples for testing, ≥2 viruses were detected in 37 samples, and 248 total virus detections were made among all samples. These included 156 influenza A(H3N2), 42 HHV6B, 32 EBV, 8 HPIV2, 2 HPIV3, 3 adenovirus, 4 HSV-1, and 1 HSV-2. Influenza A(H3N2), HHV6B, and EBV were the most frequently codetected viruses. Conclusions Our findings suggest that, in addition to mumps, clinicians should consider respiratory viral (influenza) and herpes viral etiologies for parotitis, particularly among patients without epidemiologic links to mumps cases or outbreaks.
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Affiliation(s)
- Lina I Elbadawi
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
- Bureau of Communicable Diseases, Wisconsin Division of Public Health, Madison
| | - Pamela Talley
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
- Minnesota Department of Health, St. Paul, Atlanta, Georgia
| | - Melissa A Rolfes
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Alexander J Millman
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Natalie A Kramer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lenee Blanton
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Stefanie Cole
- Michigan Department of Health and Human Services, Lansing
| | - Tonya Danz
- Wisconsin State Laboratory of Hygiene, Madison
| | - John J Dreisig
- New Hampshire Division of Public Health Services, Concord
| | - Rebecca Garten
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Thomas Haupt
- Bureau of Communicable Diseases, Wisconsin Division of Public Health, Madison
| | - Beth M Isaac
- New York City Department of Health & Mental Hygiene Bureau of Immunization, Queens
- CSTE/CDC Applied Epidemiology Fellowship, Atlanta, Georgia
| | | | - Anna Kocharian
- Bureau of Communicable Diseases, Wisconsin Division of Public Health, Madison
| | - Daniel Leifer
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Karen Martin
- Minnesota Department of Health, St. Paul, Atlanta, Georgia
| | - Lisa McHugh
- Communicable Disease Service, New Jersey Department of Health, Trenton
| | - Rebecca J McNall
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer Palm
- Minnesota Department of Health, St. Paul, Atlanta, Georgia
| | - Kay W Radford
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sara Robinson
- Maine Center for Disease Control and Prevention, Maine Department of Health and Human Services, Augusta
| | - Jennifer B Rosen
- New York City Department of Health & Mental Hygiene Bureau of Immunization, Queens
| | | | - Peter Shult
- Wisconsin State Laboratory of Hygiene, Madison
| | - Anna K Strain
- Minnesota Department of Health, St. Paul, Atlanta, Georgia
| | | | - Lori A Webber
- Maine Center for Disease Control and Prevention, Maine Department of Health and Human Services, Augusta
| | - Meghan Pearce Weinberg
- Epidemic Intelligence Service, Centers for Disease Control and Prevention, Atlanta, Georgia
- Michigan Department of Health and Human Services, Lansing
| | - David E Wentworth
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Brett L Whitaker
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Lyn Finelli
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Michael A Jhung
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Ruth Lynfield
- Minnesota Department of Health, St. Paul, Atlanta, Georgia
| | - Jeffrey P Davis
- Bureau of Communicable Diseases, Wisconsin Division of Public Health, Madison
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Flannery B, Chung JR, Belongia EA, McLean HQ, Gaglani M, Murthy K, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Foust A, Sessions W, Berman L, Barnes JR, Spencer S, Fry AM. Interim estimates of 2017-18 seasonal influenza vaccine effectiveness - United States, February 2018. Am J Transplant 2018. [DOI: 10.1111/ajt.14730] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Brendan Flannery
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - Jessie R. Chung
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | | | | | - Manjusha Gaglani
- Baylor Scott & White Health; Texas A&M University Health Science Center College of Medicine; Temple TX USA
| | - Kempapura Murthy
- Baylor Scott & White Health; Texas A&M University Health Science Center College of Medicine; Temple TX USA
| | - Richard K. Zimmerman
- University of Pittsburgh Schools of the Health Sciences and University of Pittsburgh Medical Center; Pittsburgh PA USA
| | - Mary Patricia Nowalk
- University of Pittsburgh Schools of the Health Sciences and University of Pittsburgh Medical Center; Pittsburgh PA USA
| | | | - Lisa A. Jackson
- Kaiser Permanente Washington Health Research Institute; Seattle WA USA
| | | | | | - Angie Foust
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - Wendy Sessions
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - LaShondra Berman
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - John R. Barnes
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - Sarah Spencer
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
| | - Alicia M. Fry
- Influenza Division; National Center for Immunization and Respiratory Diseases; CDC; Atlanta GA USA
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37
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Flannery B, Chung JR, Belongia EA, McLean HQ, Gaglani M, Murthy K, Zimmerman RK, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Martin ET, Foust A, Sessions W, Berman L, Barnes JR, Spencer S, Fry AM. Interim Estimates of 2017-18 Seasonal Influenza Vaccine Effectiveness - United States, February 2018. MMWR Morb Mortal Wkly Rep 2018; 67:180-185. [PMID: 29447141 PMCID: PMC5815489 DOI: 10.15585/mmwr.mm6706a2] [Citation(s) in RCA: 108] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Baranovich T, Vongphrachanh P, Ketmayoon P, Sisouk T, Chomlasack K, Khanthamaly V, Nguyen HT, Mishin VP, Marjuki H, Barnes JR, Garten RJ, Stevens J, Wentworth DE, Gubareva LV. Antiviral Drug-Resistant Influenza B Viruses Carrying H134N Substitution in Neuraminidase, Laos, February 2016. Emerg Infect Dis 2018; 23:686-690. [PMID: 28322707 PMCID: PMC5367415 DOI: 10.3201/eid2304.161876] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
In February 2016, three influenza B/Victoria/2/87 lineage viruses exhibiting 4- to 158-fold reduced inhibition by neuraminidase inhibitors were detected in Laos. These viruses had an H134N substitution in the neuraminidase and replicated efficiently in vitro and in ferrets. Current antiviral drugs may be ineffective in controlling infections caused by viruses harboring this mutation.
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Flannery B, Zimmerman RK, Gubareva LV, Garten RJ, Chung JR, Nowalk MP, Jackson ML, Jackson LA, Monto AS, Ohmit SE, Belongia EA, McLean HQ, Gaglani M, Piedra PA, Mishin VP, Chesnokov AP, Spencer S, Thaker SN, Barnes JR, Foust A, Sessions W, Xu X, Katz J, Fry AM. Enhanced Genetic Characterization of Influenza A(H3N2) Viruses and Vaccine Effectiveness by Genetic Group, 2014-2015. J Infect Dis 2016; 214:1010-9. [PMID: 27190176 DOI: 10.1093/infdis/jiw181] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/22/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND During the 2014-2015 US influenza season, expanded genetic characterization of circulating influenza A(H3N2) viruses was used to assess the impact of the genetic variability of influenza A(H3N2) viruses on influenza vaccine effectiveness (VE). METHODS A novel pyrosequencing assay was used to determine genetic group, based on hemagglutinin (HA) gene sequences, of influenza A(H3N2) viruses from patients enrolled at US Influenza Vaccine Effectiveness Network sites. VE was estimated using a test-negative design comparing vaccination among patients infected with influenza A(H3N2) viruses and uninfected patients. RESULTS Among 9710 enrollees, 1868 (19%) tested positive for influenza A(H3N2) virus; genetic characterization of 1397 viruses showed that 1134 (81%) belonged to 1 HA genetic group (3C.2a) of antigenically drifted influenza A(H3N2) viruses. Effectiveness of 2014-2015 influenza vaccination varied by influenza A(H3N2) virus genetic group from 1% (95% confidence interval [CI], -14% to 14%) against illness caused by antigenically drifted influenza A(H3N2) virus group 3C.2a viruses versus 44% (95% CI, 16%-63%) against illness caused by vaccine-like influenza A(H3N2) virus group 3C.3b viruses. CONCLUSIONS Effectiveness of 2014-2015 influenza vaccination varied by genetic group of influenza A(H3N2) virus. Changes in HA genes related to antigenic drift were associated with reduced VE.
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Affiliation(s)
| | | | | | | | - Jessie R Chung
- Influenza Division, Centers for Disease Control and Prevention Atlanta Research and Education Foundation, Georgia
| | | | | | | | - Arnold S Monto
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor
| | - Suzanne E Ohmit
- Department of Epidemiology, University of Michigan School of Public Health, Ann Arbor
| | | | | | - Manjusha Gaglani
- Baylor Scott & White Health, Texas A&M Health Science Center College of Medicine, Temple
| | - Pedro A Piedra
- Department of Molecular Virology and Microbiology, and Pediatrics, Baylor College of Medicine, Houston, Texas
| | | | | | - Sarah Spencer
- Influenza Division, Centers for Disease Control and Prevention Atlanta Research and Education Foundation, Georgia
| | - Swathi N Thaker
- Influenza Division, Centers for Disease Control and Prevention
| | - John R Barnes
- Influenza Division, Centers for Disease Control and Prevention
| | - Angie Foust
- Influenza Division, Centers for Disease Control and Prevention
| | - Wendy Sessions
- Influenza Division, Centers for Disease Control and Prevention
| | - Xiyan Xu
- Influenza Division, Centers for Disease Control and Prevention
| | - Jacqueline Katz
- Influenza Division, Centers for Disease Control and Prevention
| | - Alicia M Fry
- Influenza Division, Centers for Disease Control and Prevention
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Fry AM, Gubareva L, Garten R, Clippard J, Mishin V, Spencer S, Thaker S, Nowalk MP, Jackson ML, Jackson LA, Monto A, Zimmerman RK, Petrie JG, Belongia E, Mclean HQ, Gaglani M, Piedra P, Barnes JR, Xiyan X, Flannery B. Influenza Vaccine Effectiveness Against Drifted Versus Vaccine-Like A/H3N2 Viruses During the 2014-15 Influenza Season—US Flu VE Network. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv131.141] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Spencer S, Mishin V, Chesnokov A, Garten R, Sessions W, Foust A, Piedra P, Gaglani M, Cross R, Johnson E, Rinaldo C, Zimmerman RK, Meece J, Mclean HQ, Jackson ML, Barnes JR, Xu X, Clippard J, Thaker S, Flannery B, Gubareva L, Fry A. Novel Pyrosequencing Assay for Genetic Characterization of Influenza A(H3N2) Viruses During 2014-15 Influenza Season. Open Forum Infect Dis 2015. [DOI: 10.1093/ofid/ofv133.415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Pickering GT, Barnes JR, Bhatia R. Accurate screw arthrodesis of the distal interphalangeal joint. Ann R Coll Surg Engl 2014; 96:245-6. [PMID: 24780802 DOI: 10.1308/rcsann.2014.96.3.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- G T Pickering
- Avon Orthopaedic Centre, North Bristol NHS Trust, UK.
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Jenkins JS, Jones HR, Rojo P, Tuomi M, Jones MI, Murgas F, Barnes JR, Pavlenko Y, Ivanyuk O, Jordán A, Day-Jones AC, Ruiz MT, Pinfield DJ. Status of the Calan-Hertfordshire Extrasolar Planet Search. EPJ Web of Conferences 2013. [DOI: 10.1051/epjconf/20134705001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Monsell FP, Barnes JR, Kirubanandan R, McBride AMB. Distal tibial physeal arrest after meningococcal septicaemia: management and outcome in seven ankles. ACTA ACUST UNITED AC 2011; 93:839-43. [PMID: 21586787 DOI: 10.1302/0301-620x.93b6.26276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Survivors of infantile meningococcal septicaemia often develop progressive skeletal deformity as a result of physeal damage at many sites, particularly in the lower limb. Distal tibial physeal arrest typically occurs with sparing of the distal fibular physis leading to a rapidly progressive varus deformity. There have been reports of isolated cases of this deformity, but to our knowledge there have been no papers which specifically describe the development of the deformity and the options for treatment. Surgery to correct this deformity is complex because of the patient's age, previous scarring and the multiplanar nature of the deformity. The surgical goal is to restore leg-length equality and the mechanical axis at the end of growth. Surgery should be planned and staged throughout growth in order to achieve the best functional results. We report our experience in six patients (seven ankles) with this deformity, who were managed by corrective osteotomy using a programmable circular fixator.
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Affiliation(s)
- F P Monsell
- Bristol Royal Hospital for Children, Paul O'Gorman Building, Upper Maudlin Street, Bristol BS2 8BJ, UK.
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Monsell FP, McBride ART, Barnes JR, Kirubanandan R. Angular deformity of the ankle with sparing of the distal fibula following meningococcal septicaemia: a case series involving 14 ankles in ten children. ACTA ACUST UNITED AC 2011; 93:1131-3. [PMID: 21768642 DOI: 10.1302/0301-620x.93b8.26277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Progressive angular deformity of an extremity due to differential physeal arrest is the most common late orthopaedic sequela following meningococcal septicaemia in childhood. A total of ten patients (14 ankles) with distal tibial physeal arrest as a consequence of meningococcal septicaemia have been reviewed. Radiological analysis of their ankles has demonstrated a distinct pattern of deformity. In 13 of 14 cases the distal fibular physis was unaffected and continued distal fibular growth contributed to a varus deformity. We recommend that surgical management should take account of this consistent finding during the correction of these deformities.
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Affiliation(s)
- F P Monsell
- Bristol Royal Hospital for Children, Upper Maudlin Street, Bristol BS2 8BJ, UK.
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Donati JF, Forveille T, Cameron AC, Barnes JR, Delfosse X, Jardine MM, Valenti JA. The large-scale axisymmetric magnetic topology of a very-low-mass fully convective star. Science 2006; 311:633-5. [PMID: 16456073 DOI: 10.1126/science.1121102] [Citation(s) in RCA: 187] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Understanding how cool stars produce magnetic fields within their interiors is crucial for predicting the impact of such fields, such as the activity cycle of the Sun. In this respect, studying fully convective stars enables us to investigate the role of convective zones in magnetic field generation. We produced a magnetic map of a rapidly rotating, very-low-mass, fully convective dwarf through tomographic imaging from time series of spectropolarimetric data. Our results, which demonstrate that fully convective stars are able to trigger axisymmetric large-scale poloidal fields without differential rotation, challenge existing theoretical models of field generation in cool stars.
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Affiliation(s)
- Jean-François Donati
- Laboratoire d'Astrophysique de Toulouse-Tarbes, Observatoire Midi-Pyrénées, 14 avenue Exxxx Belin, F-31400 Toulouse, France.
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Clifford SM, Crisp D, Fisher DA, Herkenhoff KE, Smrekar SE, Thomas PC, Wynn-Williams DD, Zurek RW, Barnes JR, Bills BG, Blake EW, Calvin WM, Cameron JM, Carr MH, Christensen PR, Clark BC, Clow GD, Cutts JA, Dahl-Jensen D, Durham WB, Fanale FP, Farmer JD, Forget F, Gotto-Azuma K, Zwally HJ. The state and future of Mars polar science and exploration. Icarus 2000; 144:210-242. [PMID: 11543391 DOI: 10.1006/icar.1999.6290] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
As the planet's principal cold traps, the martian polar regions have accumulated extensive mantles of ice and dust that cover individual areas of approximately 10(6) km2 and total as much as 3-4 km thick. From the scarcity of superposed craters on their surface, these layered deposits are thought to be comparatively young--preserving a record of the seasonal and climatic cycling of atmospheric CO2, H2O, and dust over the past approximately 10(5)-10(8) years. For this reason, the martian polar deposits may serve as a Rosetta Stone for understanding the geologic and climatic history of the planet--documenting variations in insolation (due to quasiperiodic oscillations in the planet's obliquity and orbital elements), volatile mass balance, atmospheric composition, dust storm activity, volcanic eruptions, large impacts, catastrophic floods, solar luminosity, supernovae, and perhaps even a record of microbial life. Beyond their scientific value, the polar regions may soon prove important for another reason--providing a valuable and accessible reservoir of water to support the long-term human exploration of Mars. In this paper we assess the current state of Mars polar research, identify the key questions that motivate the exploration of the polar regions, discuss the extent to which current missions will address these questions, and speculate about what additional capabilities and investigations may be required to address the issues that remain outstanding.
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Affiliation(s)
- S M Clifford
- Lunar and Planetary Institute, Houston, Texas 77058, USA.
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Barnes JR. The impact of social marketing on HIV / AIDS. AIDS Anal Afr 1999; 10:8-10. [PMID: 12346539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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50
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Fu X, Barnes JR, Hossain MB, Schmitz FJ, Van Der Helm D. Novel Oxidation Products of Two Sponge-Derived Sesquiterpenes, 4α-Formamedo- and 4α-Isocyanogorgon-11-Ene. ACTA ACUST UNITED AC 1998. [DOI: 10.1080/10575639808048874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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