1
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Chard AN, Nogareda F, Regan AK, Barraza MFO, Fasce RA, Vergara N, Avendaño M, Penayo E, Vázquez C, Von Horoch M, Michel F, Alfonso A, Mogdasy C, Chiparelli H, Goñi N, Alegretti M, Loayza S, Couto P, Rodriguez A, Salas D, Fowlkes AL, Azziz-Baumgartner E. End-of-season influenza vaccine effectiveness during the Southern Hemisphere 2022 influenza season - Chile, Paraguay, and Uruguay. Int J Infect Dis 2023; 134:39-44. [PMID: 37201863 PMCID: PMC10404161 DOI: 10.1016/j.ijid.2023.05.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 02/27/2023] [Revised: 04/27/2023] [Accepted: 05/10/2023] [Indexed: 05/20/2023] Open
Abstract
OBJECTIVES This study estimated the 2022 end-of-season influenza vaccine effectiveness (VE) against severe acute respiratory illness (SARI) hospitalization in Chile, Paraguay, and Uruguay. METHODS We pooled surveillance data from SARI cases in 18 sentinel surveillance hospitals in Chile (n = 9), Paraguay (n = 2), and Uruguay (n = 7) from March 16-November 30, 2022. VE was estimated using a test-negative design and logistic regression models adjusted for country, age, sex, presence of ≥1 comorbidity, and week of illness onset. VE estimates were stratified by influenza virus type and subtype (when available) and influenza vaccine target population, categorized as children, individuals with comorbidities, and older adults, defined per countries' national immunization policies. RESULTS Among the 3147 SARI cases, there were 382 (12.1%) influenza test-positive case patients; 328 (85.9%) influenza case patients were in Chile, 33 (8.6%) were in Paraguay, and 21 (5.5%) were in Uruguay. In all countries, the predominant subtype was influenza A(H3N2) (92.6% of influenza cases). Adjusted VE against any influenza-associated SARI hospitalization was 33.8% (95% confidence interval: 15.3%, 48.2%); VE against influenza A(H3N2)-associated SARI hospitalization was 30.4% (95% confidence interval: 10.1%, 46.0%). VE estimates were similar across target populations. CONCLUSION During the 2022 influenza season, influenza vaccination reduced the odds of hospitalization among those vaccinated by one-third. Health officials should encourage influenza vaccination in accordance with national recommendations.
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Affiliation(s)
- Anna N Chard
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, USA.
| | | | - Annette K Regan
- Pan American Health Organization, Washington DC, USA; School of Nursing and Health Professions, University of San Francisco, San Francisco, USA; Fielding School of Public Health, University of California Los Angeles, Los Angeles, USA
| | | | - Rodrigo A Fasce
- Virology Department, Public Health Institute of Chile, Santiago, Chile
| | | | | | - Elena Penayo
- Ministry of Public Health and Social Welfare, Asunción, Paraguay
| | - Cynthia Vázquez
- Ministry of Public Health and Social Welfare, Asunción, Paraguay
| | - Marta Von Horoch
- Ministry of Public Health and Social Welfare, Asunción, Paraguay
| | | | | | | | | | | | | | - Sergio Loayza
- Pan American Health Organization, Washington DC, USA
| | - Paula Couto
- Pan American Health Organization, Washington DC, USA
| | | | - Daniel Salas
- Pan American Health Organization, Washington DC, USA
| | - Ashley L Fowlkes
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, USA
| | - Eduardo Azziz-Baumgartner
- Influenza Division, National Center for Immunization and Respiratory Diseases, U.S. Centers for Disease Control and Prevention, Atlanta, USA
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2
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Bruno A, Alfaro-Núñez A, de Mora D, Armas R, Olmedo M, Garcés J, Vaca MS, la Torre ED, Jarrin D, Burbano L, Salas J, Imbacuan C, Chanatasig J, Barrionuevo M, Galante MC, Salas V, Goñi N, Cristina J, Domingues CS, Montesino LO, Cardoso FG, Reischak D, Garcia-Bereguiain MA. Phylogenetic analysis reveals that the H5N1 avian influenza A outbreak in poultry in Ecuador in November 2022 is associated to the highly pathogenic clade 2.3.4.4b. Int J Infect Dis 2023; 133:27-30. [PMID: 37086864 DOI: 10.1016/j.ijid.2023.04.403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/14/2023] [Accepted: 04/17/2023] [Indexed: 04/24/2023] Open
Abstract
The ongoing H5N1 outbreak in the Americas caused by clade 2.3.4.4, is causing unprecedented impact in poultry and wild birds. In November 2022, a highly pathogenic avian influenza A outbreak was declared in poultry in Ecuador, affecting more than 1.1 million head of poultry in two farms by February 2023. Phylogenetic analysis shows that the virus clade is 2.3.4.4b, and to the best of our knowledge this is the first scientific publication reporting this clade in South America.
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Affiliation(s)
- Alfredo Bruno
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta-Pérez", Guayaquil, Ecuador; Universidad Agraria del Ecuador, Guayaquil, Ecuador.
| | - Alonzo Alfaro-Núñez
- Department of Clinical Biochemistry, Naestved Hospital, Ringstedgade 57a, 4700 Naestved, Denmark; Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen K, Denmark
| | - Doménica de Mora
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta-Pérez", Guayaquil, Ecuador
| | - Rubén Armas
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta-Pérez", Guayaquil, Ecuador; Universidad Espíritu Santo. Guayaquil. Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta-Pérez", Guayaquil, Ecuador
| | - Jimmy Garcés
- Instituto Nacional de Salud Pública e Investigación "Leopoldo Izquieta-Pérez", Guayaquil, Ecuador
| | - María Sol Vaca
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Euclides De la Torre
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - David Jarrin
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Lidia Burbano
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Johanna Salas
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Cristian Imbacuan
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - José Chanatasig
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Margoth Barrionuevo
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - María Cristina Galante
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Veronica Salas
- Agencia de Regulación y Control Fito y Zoosanitario ("Agrocalidad"), Ministerio de Agricultura y Ganadería, Ecuador
| | - Natalia Goñi
- Centro Nacional de Referencia de Influenza, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Montevideo, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Christian Steffe Domingues
- Laboratório Federal de Defesa Agropecuária, Ministério da Agricultura e Pecuária, Campinas, São Paulo, Brasil
| | - Lucas Oliveira Montesino
- Laboratório Federal de Defesa Agropecuária, Ministério da Agricultura e Pecuária, Campinas, São Paulo, Brasil
| | - Fernanda Gomes Cardoso
- Laboratório Federal de Defesa Agropecuária, Ministério da Agricultura e Pecuária, Campinas, São Paulo, Brasil
| | - Dilmara Reischak
- Laboratório Federal de Defesa Agropecuária, Ministério da Agricultura e Pecuária, Campinas, São Paulo, Brasil
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3
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Panzera Y, Cortinas MN, Marandino A, Calleros L, Bormida V, Goñi N, Techera C, Grecco S, Williman J, Ramas V, Coppola L, Mogdasy C, Chiparelli H, Pérez R. Emergence and spreading of the largest SARS-CoV-2 deletion in the Delta AY.20 lineage from Uruguay. Gene Rep 2022; 29:101703. [PMID: 36338321 PMCID: PMC9617655 DOI: 10.1016/j.genrep.2022.101703] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/24/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
Abstract
The genetic variability of SARS-CoV-2 (genus Betacoronavirus, family Coronaviridae) has been scrutinized since its first detection in December 2019. Although the role of structural variants, particularly deletions, in virus evolution is little explored, these genome changes are extremely frequent. They are associated with relevant processes, including immune escape and attenuation. Deletions commonly occur in accessory ORFs and might even lead to the complete loss of one or more ORFs. This scenario poses an interesting question about the origin and spreading of extreme structural rearrangements that persist without compromising virus viability. Here, we analyze the genome of SARS-CoV-2 in late 2021 in Uruguay and identify a Delta lineage (AY.20) that experienced a large deletion (872 nucleotides according to the reference Wuhan strain) that removes the 7a, 7b, and 8 ORFs. Deleted viruses coexist with wild-type (without deletion) AY.20 and AY.43 strains. The Uruguayan deletion is like those identified in Delta strains from Poland and Japan but occurs in a different Delta clade. Besides providing proof of the circulation of this large deletion in America, we infer that the 872-deletion arises by the consecutive occurrence of a 6-nucleotide deletion, characteristic of delta strains, and an 866-nucleotide deletion that arose independently in the AY.20 Uruguayan lineage. The largest deletion occurs adjacent to transcription regulatory sequences needed to synthesize the nested set of subgenomic mRNAs that serve as templates for transcription. Our findings support the role of transcription sequences as a hotspot for copy-choice recombination and highlight the remarkable dynamic of SARS-CoV-2 genomes.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - María Noel Cortinas
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Victoria Bormida
- Genómica, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Natalia Goñi
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Joaquín Williman
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Viviana Ramas
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Leticia Coppola
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Cristina Mogdasy
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Héctor Chiparelli
- Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Ministerio de Salud Pública, Alfredo Navarro 3051 (entrada N), 11600 Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
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4
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Panzera Y, Ramos N, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Frabasile S, Fuques E, Coppola L, Goñi N, Ramas V, Sorhouet C, Bormida V, Burgueño A, Brasesco M, Garland MR, Molinari S, Perez MT, Somma R, Somma S, Morel MN, Mogdasy C, Chiparelli H, Arbiza J, Delfraro A, Pérez R. Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion. Mem Inst Oswaldo Cruz 2022; 116:e210275. [PMID: 35019072 PMCID: PMC8752050 DOI: 10.1590/0074-02760210275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
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Affiliation(s)
- Yanina Panzera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Natalia Ramos
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Lucía Calleros
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Ana Marandino
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Gonzalo Tomás
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Claudia Techera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sofía Grecco
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sandra Frabasile
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Eddie Fuques
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Leticia Coppola
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Natalia Goñi
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Viviana Ramas
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Victoria Bormida
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Analía Burgueño
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - María Brasesco
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Rosa Garland
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Sylvia Molinari
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Teresa Perez
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Rosina Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Silvana Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Noelia Morel
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cristina Mogdasy
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Héctor Chiparelli
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Juan Arbiza
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Adriana Delfraro
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Ruben Pérez
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
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5
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Panzera Y, Ramos N, Frabasile S, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Fuques E, Goñi N, Ramas V, Coppola L, Chiparelli H, Sorhouet C, Mogdasy C, Arbiza J, Delfraro A, Pérez R. A deletion in SARS-CoV-2 ORF7 identified in COVID-19 outbreak in Uruguay. Transbound Emerg Dis 2021; 68:3075-3082. [PMID: 33501730 PMCID: PMC8014828 DOI: 10.1111/tbed.14002] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 01/20/2023]
Abstract
The analysis of genetic diversity in SARS‐CoV‐2 is the focus of several studies, providing insights into how the virus emerged and evolves. Most common changes in SARS‐CoV‐2 are single or point nucleotide substitutions; meanwhile, insertions and deletions (indels) have been identified as a less frequent source of viral genetic variability. Here, we report the emergence of a 12‐nucleotide deletion in ORF7a, resulting in a 4‐amino acid in‐frame deletion. The Δ12 variant was identified in viruses from patients of a single outbreak and represents the first report of this deletion in South American isolates. Phylogenetic analysis revealed that Δ12 strains belong to the lineage B.1.1 and clustered separated from the remaining Uruguayan strains. The ∆12 variant was detected in 14 patients of this outbreak by NGS sequencing and/or two rapid and economic methodologies: Sanger amplicon sequencing and capillary electrophoresis. The presence of strong molecular markers as the deletion described here are useful for tracking outbreaks and reveal a significant aspect of the SARS‐CoV‐2 evolution on the robustness of the virus to keep its functionality regardless loss of genetic material.
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Affiliation(s)
- Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Ramos
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sandra Frabasile
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Lucía Calleros
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Eddie Fuques
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Goñi
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Viviana Ramas
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Leticia Coppola
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Héctor Chiparelli
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Laboratorio de Biología Molecular, Mutualista Médica Uruguaya, Montevideo, Uruguay
| | - Cristina Mogdasy
- Departamento de Laboratorios de Salud Pública. Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y otros Virus Respiratorios, Montevideo, Uruguay
| | - Juan Arbiza
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Adriana Delfraro
- Sección Virología. Instituto de Biología e Instituto de Química Biológica. Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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Rivas MJ, Alegretti M, Cóppola L, Ramas V, Chiparelli H, Goñi N. Epidemiology and Genetic Variability of Circulating Influenza B Viruses in Uruguay, 2012-2019. Microorganisms 2020; 8:microorganisms8040591. [PMID: 32325860 PMCID: PMC7232498 DOI: 10.3390/microorganisms8040591] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 02/07/2023] Open
Abstract
Influenza B viruses (IBV) are an important cause of morbidity and mortality during interpandemic periods in the human population. Two phylogenetically distinct IBV lineages, B/Yamagata and B/Victoria, co-circulate worldwide and they present challenges for vaccine strain selection. Until the present study, there was little information regarding the pattern of the circulating strains of IBV in Uruguay. A subset of positive influenza B samples from influenza-like illness (ILI) outpatients and severe acute respiratory illness (SARI) inpatients detected in sentinel hospitals in Uruguay during 2012–2019 were selected. The sequencing of the hemagglutinin (HA) and neuraminidase (NA) genes showed substitutions at the amino acid level. Phylogenetic analysis reveals the co-circulation of both lineages in almost all seasonal epidemics in Uruguay, and allows recognizing a lineage-level vaccine mismatch in approximately one-third of the seasons studied. The epidemiological results show that the proportion of IBV found in ILI was significantly higher than the observed in SARI cases across different groups of age (9.7% ILI, 3.2% SARI) and patients between 5–14 years constituted the majority (33%) of all influenza B infection (p < 0.05). Interestingly, we found that individuals >25 years were particularly vulnerable to Yamagata lineage infections.
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Affiliation(s)
- María José Rivas
- Centro Nacional de Referencia de Influenza, Unidad de Virología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud, Montevideo 11600, Uruguay; (M.J.R.); (L.C.); (V.R.); (H.C.)
| | - Miguel Alegretti
- Departamento de Vigilancia en Salud, Ministerio de Salud, Montevideo 11200, Uruguay;
| | - Leticia Cóppola
- Centro Nacional de Referencia de Influenza, Unidad de Virología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud, Montevideo 11600, Uruguay; (M.J.R.); (L.C.); (V.R.); (H.C.)
| | - Viviana Ramas
- Centro Nacional de Referencia de Influenza, Unidad de Virología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud, Montevideo 11600, Uruguay; (M.J.R.); (L.C.); (V.R.); (H.C.)
| | - Héctor Chiparelli
- Centro Nacional de Referencia de Influenza, Unidad de Virología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud, Montevideo 11600, Uruguay; (M.J.R.); (L.C.); (V.R.); (H.C.)
| | - Natalia Goñi
- Centro Nacional de Referencia de Influenza, Unidad de Virología, Departamento de Laboratorios de Salud Pública, Ministerio de Salud, Montevideo 11600, Uruguay; (M.J.R.); (L.C.); (V.R.); (H.C.)
- Correspondence: ; Tel.: +598-99191211
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Leite JA, Resende P, Araya JL, Barrera GB, Baumeister E, Caicedo AB, Coppola L, de Mello WA, de Mora D, Cordeiro dos Santos M, Fasce R, Fernández J, Goñi N, Martínez IL, Mayhua JO, Motta F, Nuñez MCH, Ojeda J, Ortega MJ, Ospitia E, de Paiva TM, Pontoriero A, Porras HB, Quinonez JAD, Ramas V, Ramírez JB, Santos KCDO, Siqueira MM, Vàzquez C, Palekar R. Genetic evolution of influenza viruses among selected countries in Latin America, 2017-2018. PLoS One 2020; 15:e0227962. [PMID: 32155152 PMCID: PMC7064222 DOI: 10.1371/journal.pone.0227962] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/03/2020] [Indexed: 02/01/2023] Open
Abstract
OBJECTIVE Since the 2009 influenza pandemic, Latin American (LA) countries have strengthened their influenza surveillance systems. We analyzed influenza genetic sequence data from the 2017 through 2018 Southern Hemisphere (SH) influenza season from selected LA countries, to map the availability of influenza genetic sequence data from, and to describe, the 2017 through 2018 SH influenza seasons in LA. METHODS We analyzed influenza A/H1pdm09, A/H3, B/Victoria and B/Yamagata hemagglutinin sequences from clinical samples from 12 National Influenza Centers (NICs) in ten countries (Argentina, Brazil, Chile, Colombia, Costa Rica, Ecuador, Mexico, Paraguay, Peru and Uruguay) with a collection date from epidemiologic week (EW) 18, 2017 through EW 43, 2018. These sequences were generated by the NIC or the WHO Collaborating Center (CC) at the U.S Centers for Disease Control and Prevention, uploaded to the Global Initiative on Sharing All Influenza Data (GISAID) platform, and used for phylogenetic reconstruction. FINDINGS Influenza hemagglutinin sequences from the participating countries (A/H1pdm09 n = 326, A/H3 n = 636, B n = 433) were highly concordant with the genetic groups of the influenza vaccine-recommended viruses for influenza A/H1pdm09 and influenza B. For influenza A/H3, the concordance was variable. CONCLUSIONS Considering the constant evolution of influenza viruses, high-quality surveillance data-specifically genetic sequence data, are important to allow public health decision makers to make informed decisions about prevention and control strategies, such as influenza vaccine composition. Countries that conduct influenza genetic sequencing for surveillance in LA should continue to work with the WHO CCs to produce high-quality genetic sequence data and upload those sequences to open-access databases.
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Affiliation(s)
- Juliana Almeida Leite
- Pan American Health Organization (PAHO/WHO), Washington, DC, United States of America
| | - Paola Resende
- Laboratorio de Virus Respiratorio, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jenny Lara Araya
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica
| | - Gisela Badillo Barrera
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, Mexico, Mexico
| | - Elsa Baumeister
- Instituto Nacional de Enfermedades Infecciosas—Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) "Dr. Carlos G. Malbran", Buenos Aires, Argentina
| | - Alfredo Bruno Caicedo
- Instituto Nacional de Investigación en Salud Pública (INSPI), Guayaquil, Guayas, Ecuador
| | - Leticia Coppola
- Departamento de Laboratorio de Salud Publica (DLSP), Montevideo, Montevideo, Uruguay
| | | | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública (INSPI), Guayaquil, Guayas, Ecuador
| | | | - Rodrigo Fasce
- Instituto de Salud Pública de Chile (ISPCH), Santiago, Santiago, Chile
| | - Jorge Fernández
- Instituto de Salud Pública de Chile (ISPCH), Santiago, Santiago, Chile
| | - Natalia Goñi
- Departamento de Laboratorio de Salud Publica (DLSP), Montevideo, Montevideo, Uruguay
| | - Irma López Martínez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, Mexico, Mexico
| | | | - Fernando Motta
- Laboratorio de Virus Respiratorio, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Jenny Ojeda
- Ministerio de Salud Pública, Quito, Pichincha, Ecuador
| | - María José Ortega
- Laboratorio Central de Salud Pública (LCSP), Ascuncion, Distrito Capital, Paraguay
| | - Erika Ospitia
- Instituto Nacional de Salud (INS), Bogota, Cundinamarca, Colombia
| | | | - Andrea Pontoriero
- Instituto Nacional de Enfermedades Infecciosas—Administración Nacional de Laboratorios e Institutos de Salud (INEI-ANLIS) "Dr. Carlos G. Malbran", Buenos Aires, Argentina
| | - Hebleen Brenes Porras
- Instituto Costarricense de Investigación y Enseñanza en Nutrición y Salud (INCIENSA), Tres Ríos, Cartago, Costa Rica
| | - Jose Alberto Diaz Quinonez
- Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE), Ciudad de México, Mexico, Mexico
- Division of Postgraduate Studies, Faculty of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Viviana Ramas
- Departamento de Laboratorio de Salud Publica (DLSP), Montevideo, Montevideo, Uruguay
| | | | | | - Marilda Mendonça Siqueira
- Laboratorio de Virus Respiratorio, Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cynthia Vàzquez
- Laboratorio Central de Salud Pública (LCSP), Ascuncion, Distrito Capital, Paraguay
| | - Rakhee Palekar
- Pan American Health Organization (PAHO/WHO), Washington, DC, United States of America
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Palekar RS, Rolfes MA, Arriola CS, Acosta BO, Guidos PA, Vargas XB, Bancej C, Ramirez JB, Baumeister E, Bruno A, Cabello MA, Chen J, Couto P, Junior FJDP, Fasce R, Ferreira de Almeida W, Solorzano VEF, Ramírez CF, Goñi N, Isaza de Moltó Y, Lara J, Malo DC, Medina Osis JL, Mejía H, Castillo LM, Mustaquim D, Nwosu A, Ojeda J, Samoya AP, Pulido PA, Ramos Hernandez HM, Lopez RR, Rodriguez A, Saboui M, Bolanos HS, Santoro A, Silvera JE, Sosa P, Sotomayor V, Suarez L, Von Horoch M, Azziz-Baumgartner E. Burden of influenza-associated respiratory hospitalizations in the Americas, 2010-2015. PLoS One 2019; 14:e0221479. [PMID: 31490961 PMCID: PMC6730873 DOI: 10.1371/journal.pone.0221479] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/07/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Despite having influenza vaccination policies and programs, countries in the Americas underutilize seasonal influenza vaccine, in part because of insufficient evidence about severe influenza burden. We aimed to estimate the annual burden of influenza-associated respiratory hospitalizations in the Americas. METHODS Thirty-five countries in the Americas with national influenza surveillance were invited to provide monthly laboratory data and hospital discharges for respiratory illness (International Classification of Diseases 10th edition J codes 0-99) during 2010-2015. In three age-strata (<5, 5-64, and ≥65 years), we estimated the influenza-associated hospitalizations rate by multiplying the monthly number of respiratory hospitalizations by the monthly proportion of influenza-positive samples and dividing by the census population. We used random effects meta-analyses to pool age-group specific rates and extrapolated to countries that did not contribute data, using pooled rates stratified by age group and country characteristics found to be associated with rates. RESULTS Sixteen of 35 countries (46%) contributed primary data to the analyses, representing 79% of the America's population. The average pooled rate of influenza-associated respiratory hospitalization was 90/100,000 population (95% confidence interval 61-132) among children aged <5 years, 21/100,000 population (13-32) among persons aged 5-64 years, and 141/100,000 population (95-211) among persons aged ≥65 years. We estimated the average annual number of influenza-associated respiratory hospitalizations in the Americas to be 772,000 (95% credible interval 716,000-829,000). CONCLUSIONS Influenza-associated respiratory hospitalizations impose a heavy burden on health systems in the Americas. Countries in the Americas should use this information to justify investments in seasonal influenza vaccination-especially among young children and the elderly.
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Affiliation(s)
- Rakhee S. Palekar
- Pan American Health Organization/World Health Organization, Washington, DC, United States of America
- * E-mail:
| | - Melissa A. Rolfes
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - C. Sofia Arriola
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | - Belsy O. Acosta
- Department of Virology, “Pedro Kouri” Institute of Tropical Medicine, Havana, Cuba
| | | | | | | | | | - Elsa Baumeister
- National Reference Laboratory for Viral Respiratory Infections and National Influenza Center, Buenos Aires, Argentina
| | - Alfredo Bruno
- National Institute of Public Health Research, Guayaquil, Ecuador
| | | | - Jufu Chen
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
- Battelle Memorial Institute, Atlanta, GA, United States of America
| | - Paula Couto
- Pan American Health Organization/World Health Organization, Washington, DC, United States of America
| | | | | | | | | | | | - Natalia Goñi
- Department of Public Health Laboratories, Montevideo, Uruguay
| | | | - Jenny Lara
- Costa Rican Institute of Research and Education in Nutrition and Health, Cartago, Costa Rica
| | | | - José L. Medina Osis
- National Center of Epidemiology, Prevention, and Control of Diseases, Lima, Peru
| | | | | | - Desiree Mustaquim
- Centers for Disease Control and Prevention, Atlanta, GA, United States of America
| | | | | | | | | | | | | | - Angel Rodriguez
- Pan American Health Organization/World Health Organization, Washington, DC, United States of America
| | | | | | - Adrián Santoro
- Directorate of Statistics and Health Information, Buenos Aires, Argentina
| | | | - Paulina Sosa
- Pan American Health Organization/World Health Organization, Washington, DC, United States of America
| | | | | | - Marta Von Horoch
- Ministry of Public Health and Social Welfare, Asuncion, Paraguay
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Olson RJ, Young JW, Ménard F, Potier M, Allain V, Goñi N, Logan JM, Galván-Magaña F. Bioenergetics, Trophic Ecology, and Niche Separation of Tunas. Adv Mar Biol 2016; 74:199-344. [PMID: 27573052 DOI: 10.1016/bs.amb.2016.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 06/06/2023]
Abstract
Tunas are highly specialized predators that have evolved numerous adaptations for a lifestyle that requires large amounts of energy consumption. Here we review our understanding of the bioenergetics and feeding dynamics of tunas on a global scale, with an emphasis on yellowfin, bigeye, skipjack, albacore, and Atlantic bluefin tunas. Food consumption balances bioenergetics expenditures for respiration, growth (including gonad production), specific dynamic action, egestion, and excretion. Tunas feed across the micronekton and some large zooplankton. Some tunas appear to time their life history to take advantage of ephemeral aggregations of crustacean, fish, and molluscan prey. Ontogenetic and spatial diet differences are substantial, and significant interdecadal changes in prey composition have been observed. Diet shifts from larger to smaller prey taxa highlight ecosystem-wide changes in prey availability and diversity and provide implications for changing bioenergetics requirements into the future. Where tunas overlap, we show evidence of niche separation between them; resources are divided largely by differences in diet percentages and size ranges of prey taxa. The lack of long-term data limits the ability to predict impacts of climate change on tuna feeding behaviour. We note the need for systematic collection of feeding data as part of routine monitoring of these species, and we highlight the advantages of using biochemical techniques for broad-scale analyses of trophic relations. We support the continued development of ecosystem models, which all too often lack the regional-specific trophic data needed to adequately investigate climate and fishing impacts.
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Affiliation(s)
- R J Olson
- Inter-American Tropical Tuna Commission, La Jolla, CA, United States.
| | - J W Young
- CSIRO Marine and Atmospheric Research, Hobart, TAS, Australia
| | - F Ménard
- Institut de Recherche pour le Développement (IRD), Mediterranean Institute of Oceanography (Aix-Marseille Université, CNRS, IRD, Université de Toulon), Marseille, France
| | - M Potier
- IRD, UMR MARBEC (IRD, UM, Ifremer, CNRS), Sète cedex, France
| | - V Allain
- Pacific Community (SPC), Nouméa cedex, New Caledonia
| | - N Goñi
- AZTI-Tecnalia/Marine Research, Pasaia, Gipuzkoa, Spain
| | - J M Logan
- Massachusetts Division of Marine Fisheries, New Bedford, MA, United States
| | - F Galván-Magaña
- Instituto Politécnico Nacional, Centro Interdisciplinario de Ciencias Marinas, La Paz, Baja California Sur, Mexico
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10
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Macías-Murelaga B, Rodriguez-Agirretxe I, Bascarán L, Goñi N, Mendicute J. [Acute idiopathic blind spot enlargement syndrome associated with choroidal neovascularization]. ACTA ACUST UNITED AC 2013; 88:450-2. [PMID: 24157324 DOI: 10.1016/j.oftal.2012.12.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 01/04/2012] [Revised: 11/21/2012] [Accepted: 12/18/2012] [Indexed: 11/17/2022]
Abstract
CLINICAL CASE A 17 year old female consulting due to photopsia and a sudden loss of visual field in left eye (OS), with previous contralateral choroidal neovascularization. The examination suggested an acute idiopathic blind spot syndrome. The progress without treatment was favorable, with a reduction in the scotoma and without a worsening of her visual acuity. DISCUSSION This case report is about an unusual and benign syndrome, typical of young women. Differential diagnosis must be made between the evanescent white dot syndrome and the acute zonal occult outer retinopathy. To our knowledge, this is the first published case associated with choroidal neovascularization, a fact that leads us to question its benignancy.
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Affiliation(s)
- B Macías-Murelaga
- Servicio de Oftalmología, Hospital Donostia, Donostia-San Sebastián, España.
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11
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Goñi N, Iriarte A, Comas V, Soñora M, Moreno P, Moratorio G, Musto H, Cristina J. Pandemic influenza A virus codon usage revisited: biases, adaptation and implications for vaccine strain development. Virol J 2012; 9:263. [PMID: 23134595 PMCID: PMC3543350 DOI: 10.1186/1743-422x-9-263] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [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: 02/23/2012] [Accepted: 11/02/2012] [Indexed: 11/20/2022] Open
Abstract
Background Influenza A virus (IAV) is a member of the family Orthomyxoviridae and contains eight segments of a single-stranded RNA genome with negative polarity. The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 IAV strain (H1N1pdm) in Mexico and USA. Understanding the extent and causes of biases in codon usage is essential to the understanding of viral evolution. A comprehensive study to investigate the effect of selection pressure imposed by the human host on the codon usage of an emerging, pandemic IAV strain and the trends in viral codon usage involved over the pandemic time period is much needed. Results We performed a comprehensive codon usage analysis of 310 IAV strains from the pandemic of 2009. Highly biased codon usage for Ala, Arg, Pro, Thr and Ser were found. Codon usage is strongly influenced by underlying biases in base composition. When correspondence analysis (COA) on relative synonymous codon usage (RSCU) is applied, the distribution of IAV ORFs in the plane defined by the first two major dimensional factors showed that different strains are located at different places, suggesting that IAV codon usage also reflects an evolutionary process. Conclusions A general association between codon usage bias, base composition and poor adaptation of the virus to the respective host tRNA pool, suggests that mutational pressure is the main force shaping H1N1 pdm IAV codon usage. A dynamic process is observed in the variation of codon usage of the strains enrolled in these studies. These results suggest a balance of mutational bias and natural selection, which allow the virus to explore and re-adapt its codon usage to different environments. Recoding of IAV taking into account codon bias, base composition and adaptation to host tRNA may provide important clues to develop new and appropriate vaccines.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo, 11400, Uruguay
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12
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Goñi N, Moratorio G, Coppola L, Ramas V, Comas V, Soñora M, Chiparelli H, Cristina J. Bayesian coalescent analysis of pandemic H1N1 influenza A virus circulating in the South American region. Virus Res 2012; 170:91-101. [PMID: 22983300 DOI: 10.1016/j.virusres.2012.09.002] [Citation(s) in RCA: 2] [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] [Received: 05/17/2012] [Revised: 09/04/2012] [Accepted: 09/06/2012] [Indexed: 12/27/2022]
Abstract
The first influenza pandemic of this century was declared in April of 2009, with the emergence of a novel H1N1 influenza A virus strain (H1N1pdm). Understanding the evolution of H1N1pdm populations within the South American region is essential for studying global diversification, emergence, resistance and vaccine efficacy. In order to gain insight into these matters, we have performed a Bayesian coalescent Markov Chain Monte Carlo analysis of hemagglutinin (HA) and neuraminidase (NA) gene sequences of all available and comparable HA and NA sequences obtained from H1N1pdm IAV circulating in the South American region. High evolutionary rates and fast population growths characterize the population dynamics of H1N1pdm strains in this region of the world. A significant contribution of first codon position to the mean evolutionary rate was found for both genes studied, revealing a high contribution of non-synonymous substitutions to the mean substitution rate. In the 178days period covered by these studies, substitutions in all HA epitope regions can be observed. HA substitutions D239G/N and Q310H have been observed only in Brazilian patients. While substitution D239G/N is not particularly associated to a specific genetic lineage, all strains bearing substitution Q310H were assigned to clade 6, suggesting a founder effect. None of the substitutions found in the NA proteins of H1N1pdm strains isolated in South America appears sufficiently close to affect the drug binding pocket for the three NA inhibitor antivirals tested. A more detailed analysis of NA proteins revealed epitope differences among 2010 vaccine and H1N1pdm IAV strains circulating in the South American region.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Igua 4225, 11400 Montevideo, Uruguay
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13
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Goñi N, Fajardo A, Moratorio G, Colina R, Cristina J. Modeling gene sequences over time in 2009 H1N1 influenza A virus populations. Virol J 2009; 6:215. [PMID: 19961611 PMCID: PMC2794274 DOI: 10.1186/1743-422x-6-215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [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: 09/28/2009] [Accepted: 12/04/2009] [Indexed: 11/11/2022] Open
Abstract
Background A sudden emergence of Influenza A Virus (IAV) infections with a new pandemic H1N1 IAV is taking place since April of 2009. In order to gain insight into the mode of evolution of these new H1N1 strains, we performed a Bayesian coalescent Markov chain Monte Carlo (MCMC) analysis of full-length neuraminidase (NA) gene sequences of 62 H1N1 IAV strains (isolated from March 30th to by July 28th, 2009). Results The results of these studies revealed that the expansion population growth model was the best to fit the sequence data. A mean of evolutionary change of 7.84 × 10-3 nucleotide substitutions per site per year (s/s/y) was obtained for the NA gene. A significant contribution of first codon position to this mean rate was observed. Maximum clade credibility trees revealed a rapid diversification of NA genes in different genetic lineages, all of them containing Oseltamivir-resistant viruses of very recent emergence. Mapping of naturally occurring amino acid substitutions in the NA protein from 2009 H1N1 IAV circulating in 62 different patients revealed that substitutions are distributed all around the surface of the molecule, leaving the hydrophobic core and the catalytic site essentially untouched. Conclusion High evolutionary rates and fast population growth have contributed to the initial transmission dynamics of 2009 H1N1 IAV. Naturally occurring substitutions are preferentially located at the protein surface and do not interfere with the NA active site. Antigenic regions relevant for vaccine development can differ from previous vaccine strains and vary among patients.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Facultad de Ciencias, Centro de Investigaciones Nucleares, Igua 4225, 11400 Montevideo, Uruguay
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14
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Goñi N, Russi J, Cristina J. Human influenza A viruses isolated in South America: genetic relations, adamantane resistance and vaccine strain match. Infect Genet Evol 2008; 9:229-34. [PMID: 19095085 DOI: 10.1016/j.meegid.2008.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2008] [Revised: 11/12/2008] [Accepted: 11/13/2008] [Indexed: 11/28/2022]
Abstract
In order to gain insight into the genetic relations among H3N2 Influenza A virus (IAV) circulating in the South American region from 1999 to 2007, to investigate the presence of adamantane-resistant strains in this region, and to establish the genetic relations among that strains and vaccine strains recommended for the Southern hemisphere, 11 haemagglutinin (HA) H3 IAV sequences obtained from Uruguayan patients were aligned with corresponding sequences from 68 H3 IAV strains isolated in South America and 9 H3 IAV vaccine strains. Maximum likelihood phylogenetic tree analysis was performed using the GTR evolutionary model. The results of these studies indicate that multiple clades co-circulate during most influenza seasons in South America. Strikingly, one strain isolated in Uruguay in 2005 and all strains isolated in that country during the 2007 season bear an HA adamantane-resistant polymorphism. No other strain isolated in South America previous to the 2005 season bears that HA characteristic amino acid change. Only vaccine strains recommended for the 2007 season were assigned to the same cluster with all available IAV isolated in South America for that season. Evolution of IAV in this region appears to be shaped by re-introduction of new strains.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
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15
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Goñi N, Baz M, Ruchansky D, Coppola L, Russi J, Cristina J. Influenza B viruses isolated in Uruguay during the 2002-2005 seasons: genetic relations and vaccine strain match. Virus Res 2006; 123:100-4. [PMID: 16987563 DOI: 10.1016/j.virusres.2006.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 08/01/2006] [Accepted: 08/02/2006] [Indexed: 11/20/2022]
Abstract
Monitoring antigenic and genetic variations of circulating influenza viruses is critical for the selection of annual vaccine strains. In order to gain insight into the molecular evolution of Influenza B viruses (IBV) isolated in Uruguay in 2002 and 2005 outbreaks, antigenic and phylogenetic studies were carried out for the Hemagglutinin (HA) gene. Antigenic relations among Uruguayan and reference strains isolated elsewhere were performed by means of hemagglutination inhibition assays (HAI). Genetic relations of HA genes from Uruguayan as well as 41 IBV strains isolated elsewhere were established by means of the construction of phylogenetic trees. HAI assays showed a distant antigenic relationship among the 2002 Uruguayan isolates and the 2002 vaccine strain B/Sichuan/379/99. Phylogenetic analysis also revealed a distant genetic relationship among Uruguayan and 2002 vaccine strains. All 2005 IBV Uruguayan strains were both antigenically and genetically related to B/Victoria lineage-viruses. The results of these studies revealed that 2002 IBV Uruguayan strains have a distant antigenic and genetic relation with the 2002 IBV vaccine strain used in Uruguay. The high rate of susceptible individuals in the youngest cohort (<25 years) might be related to the fact that the B/Victoria lineage-viruses were not previously circulating in Uruguay.
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Affiliation(s)
- Natalia Goñi
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Iguá 4225, 11400 Montevideo, Uruguay
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