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Ospina-Jimenez AF, Gomez AP, Rincon-Monroy MA, Ortiz L, Perez DR, Peña M, Ramirez-Nieto G. Sequence-Based Antigenic Analyses of H1 Swine Influenza A Viruses from Colombia (2008-2021) Reveals Temporal and Geographical Antigenic Variations. Viruses 2023; 15:2030. [PMID: 37896808 PMCID: PMC10612065 DOI: 10.3390/v15102030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 09/22/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Swine influenza is a respiratory disease that affects the pork industry and is a public health threat. It is caused by type A influenza virus (FLUAV), which continuously undergoes genetic and antigenic variations. A large amount of information regarding FLUAV in pigs is available worldwide, but it is limited in Latin America. The HA sequences of H1 subtype FLUAV-positive samples obtained from pigs in Colombia between 2008-2021 were analyzed using sequence-based antigenic cartography and N-Glycosylation analyses. Of the 12 predicted global antigenic groups, Colombia contained five: four corresponding to pandemic strains and one to the classical swine H1N1 clade. Circulation of these clusters was observed in some regions during specific years. Ca2 was the immunodominant epitope among Colombian viruses. The counts of N-Glycosylation motifs were associated with the antigenic cluster ranging from three to five. The results show for the first time the existence of antigenic diversity of FLUAV in Colombia and highlight the impact of spatial and temporal factors on this diversity. This study provides information about FLUAV variability in pigs under natural conditions in the absence of vaccination and emphasizes the need for surveillance of its phylogenetic and antigenic characteristics.
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Affiliation(s)
- Andres F. Ospina-Jimenez
- Grupo de Investigación en Microbiología y Epidemiología, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (A.F.O.-J.); (A.P.G.); (M.A.R.-M.)
| | - Arlen P. Gomez
- Grupo de Investigación en Microbiología y Epidemiología, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (A.F.O.-J.); (A.P.G.); (M.A.R.-M.)
| | - Maria A. Rincon-Monroy
- Grupo de Investigación en Microbiología y Epidemiología, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (A.F.O.-J.); (A.P.G.); (M.A.R.-M.)
- National Veterinary Diagnostics Laboratory, Colombian Agricultural Institute (ICA), Bogotá 110931, Colombia
| | - Lucia Ortiz
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (L.O.); (D.R.P.)
| | - Daniel R. Perez
- Poultry Diagnostic and Research Center, Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA 30602, USA; (L.O.); (D.R.P.)
| | - Mario Peña
- Asociación Colombiana de Porcicultores Porkcolombia—FNP, Bogotá 111311, Colombia;
| | - Gloria Ramirez-Nieto
- Grupo de Investigación en Microbiología y Epidemiología, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Bogotá 111321, Colombia; (A.F.O.-J.); (A.P.G.); (M.A.R.-M.)
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Kuzmanovska M, Boshevska G, Janchevska E, Buzharova T, Simova M, Peshnacka A, Nikolovska G, Kochinski D, Ilioska RS, Stavridis K, Mikikj V, Kuzmanovska G, Memeti S, Gjorgoski I. A Comprehensive Molecular and Epidemiological Characterization of Influenza Viruses Circulating 2016-2020 in North Macedonia. Front Microbiol 2021; 12:713408. [PMID: 34745027 PMCID: PMC8567633 DOI: 10.3389/fmicb.2021.713408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Accepted: 09/27/2021] [Indexed: 11/16/2022] Open
Abstract
Influenza viruses know no boundaries, representing an example of rapid virus evolution combined with pressure exerted by the host’s immune system. Seasonal influenza causes 4–50 million symptomatic cases in the EU/EEA each year, with a global death toll reaching 650,000 deaths. That being the case, in 2014 North Macedonia introduced the sentinel surveillance in addition to the existing influenza surveillance in order to obtain more precise data on the burden of disease, circulating viruses and to implement timely preventive measures. The aims of this study were to give a comprehensive virological and epidemiological overview of four influenza seasons (2016–2020), assess the frequency and distribution of influenza circulating in North Macedonia and to carry out molecular and phylogenetic analyses of the hemagglutinin (HA) and neuraminidase (NA) genes of influenza A(H1N1)pdm09, A(H3N2) from ILI and SARI patients. Our results showed that out of 1,632 tested samples, 46.4% were influenza positive, with influenza A(H1N1)pdm09 accounting for the majority of cases (44%), followed by influenza B (32%) and A(H3N2) (17%). By comparing the sentinel surveillance system to the routine surveillance system, we showed that the newly applied system works efficiently and gives great results in the selection of cases. Statistically significant differences (p = < 0.0000001) were observed when comparing the number of reported ILI cases among patients aged 0–4, 5–14, 15–29, and 30–64 years to the reference age group. The phylogenetic analysis of the HA sequences unveiled the resemblance of mutations circulating seasonally worldwide, with a vast majority of circulating viruses belonging to subclade 6B.1A. The PROVEAN analysis showed that the D187A substitution in the receptor binding site (RBS) of the A(H1N1)pdm09 HA has a deleterious effect on the its function. The A(H3N2) viruses fell into the 3C.2a and 3C.3a throughout the analyzed seasons. Molecular characterization revealed that various substitutions in the A(H3N2) viruses gradually replaced the parental variant in subsequent seasons before becoming the dominant variant. With the introduction of sentinel surveillance, accompanied by the advances made in whole-genome sequencing and vaccine therapeutics, public health officials can now modify their approach in disease management and intervene effectively and in a timely manner to prevent major morbidity and mortality from influenza.
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Affiliation(s)
- Maja Kuzmanovska
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | | | | | - Teodora Buzharova
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Milica Simova
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Aneta Peshnacka
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Gordana Nikolovska
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Dragan Kochinski
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | | | - Kristina Stavridis
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Vladimir Mikikj
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | | | - Shaban Memeti
- Laboratory of Virology, Institute of Public Health, Skopje, North Macedonia
| | - Icko Gjorgoski
- Faculty of Natural Sciences and Mathematics, Skopje, North Macedonia
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Zhao XN, Zhang HJ, Li D, Zhou JN, Chen YY, Sun YH, Adeola AC, Fu XQ, Shao Y, Zhang ML. Whole-genome sequencing reveals origin and evolution of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018. PLoS One 2020; 15:e0234869. [PMID: 32579578 PMCID: PMC7314029 DOI: 10.1371/journal.pone.0234869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 06/03/2020] [Indexed: 11/18/2022] Open
Abstract
The continuous variation of the seasonal influenza viruses, particularly A(H1N1)pdm09, persistently threatens human life and health around the world. In local areas of southwest china, the large time-scale genomic research on A(H1N1)pdm09 is still insufficient. Here, we sequenced 45 whole-genome sequences of influenza A(H1N1)pdm09 viruses in Lincang, China, from 2014 to 2018, by next-generation sequencing technology to characterize molecular mechanisms of their origin and evolution. Our phylogenetic analyses suggest that the A(H1N1)pdm09 strains circulating in Lincang belong to clade 6B and the subclade 6B.1A predominates in 2018. Further, the strains in 2018 possess elevated evolutionary rate as compared to strains in other years. Several newly emerged mutations for HA (hemagglutinin) in 2018 are revealed (i.e., S183P and R221K). Intriguingly, the substitution R221K falls into the RBS (receptor binding site) of HA protein, which could affect antigenic properties of influenza A(H1N1)pdm09 viruses, and another substitution S183P near to RBS with a high covering frequency (11/14 strains) in 2018 is exactly located at the epitope B. Notably, the NA (neuraminidase) protein harbors a new mutation I23T, potentially involved in N-glycosylation. Based on the background with a higher evolutionary rate in 2018 strains, we deeply evaluate the potential vaccine efficacy against Lincang strains and discover a substantive decline of the vaccine efficacy in 2018. Our analyses reaffirm that the real-time molecular surveillance and timely updated vaccine strains for prevention and control of influenza A(H1N1)pdm09 are crucial in the future.
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Affiliation(s)
- Xiao-Nan Zhao
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Han-Ju Zhang
- Lincang Center for Disease Control and Prevention, Lincang, Yunnan, China
| | - Duo Li
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Jie-Nan Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yao-Yao Chen
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yan-Hong Sun
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Adeniyi C. Adeola
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
| | - Xiao-Qing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
| | - Yong Shao
- State Key Laboratory of Genetic Resources and Evolution, Chinese Academy of Sciences, Kunming Institute of Zoology, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
| | - Mei-Ling Zhang
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Center for Disease Control and Prevention, Kunming, Yunnan, China
- * E-mail: (MLZ); (YS)
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Lope P, Maribel H, Egma M, Henri B, Carlos P. Characterization of influenza A(H1N1)pdm09 isolates of Peru using HRM, a post PCR molecular biology method. Bioinformation 2019; 15:640-645. [PMID: 31787813 PMCID: PMC6859703 DOI: 10.6026/97320630015640] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 10/06/2019] [Accepted: 10/07/2019] [Indexed: 11/23/2022] Open
Abstract
Influenza caused by A(H1N1)pdm09 is a public health issue with severe conditions in vulnerable populations leading to death. Therefore, it is of interest to characterize and monitor influenza A(H1N1)pdm09 genotypes using High Resolution Melting (HRM), a post PCR molecular biology method. We used HRM analysis (using RotorGene Q thermocycler) to characterize A(H1N1)pdm09 genotypes from several places of Peru. RNA was purified from nasal and pharyngeal swab samples referred to LRNVR-INS, synthesized cDNA, and then the hemagglutinin gene and matrix fragment were amplified. Thus, 287 samples positive for influenza A(H1N1)pdm09 were identified across Peru where places like Lima, Piura, and Arequipa documented highest number of cases. The HRM data was analyzed and results showed different profiles which were further grouped into four genotypes for the HA (A, B, C, D) and 3 for the M (a, b, c) genes. We also report ten genotypes (I-X) of virus using combined HA (hemagglutinin) and M gene profiles representing a national geography. The prevalent genotypes are I and II with a frequency of 35.89% (103) and 29.27% (84), respectively linking with severe acute respiratory infection.
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Affiliation(s)
- Priscila Lope
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
- Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Huaringa Maribel
- Laboratorio de Referencia Nacional de Virus Respiratorio, Centro Nacional de Salud Publica, Instituto Nacional de Salud, Lima, Peru
| | - Mayta Egma
- Laboratorio de virologia. Universidad Nacional Mayor de San Marcos. Lima. Peru
| | - Bailon Henri
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
| | - Padilla Carlos
- Laboratorio de Referencia Nacional de Biotecnologia y Biologia Molecular. Centro Nacional de Salud Publica. Instituto Nacional de Salud. Lima. Peru
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