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Siegers JY, Wille M, Yann S, Tok S, Sin S, Chea S, Porco A, Sours S, Chim V, Chea S, Chhel K, Tum S, Sorn S, Hak M, Thielen P, Dhanasekaran V, Karlsson EA. Detection and phylogenetic analysis of contemporary H14N2 Avian influenza A virus in domestic ducks in Southeast Asia (Cambodia). Emerg Microbes Infect 2024; 13:2297552. [PMID: 38112157 PMCID: PMC11025406 DOI: 10.1080/22221751.2023.2297552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 12/17/2023] [Indexed: 12/20/2023]
Abstract
Avian influenza virus (AIV) in Asia is a complex system with numerous subtypes and a highly porous wild birds-poultry interface. Certain AIV subtypes, such as H14, are underrepresented in current surveillance efforts, leaving gaps in our understanding of their ecology and evolution. The detection of rare subtype H14 in domestic ducks in Southeast Asia comprises a geographic region and domestic bird population previously unassociated with this subtype. These H14 viruses have a complex evolutionary history involving gene reassortment events. They share sequence similarity to AIVs endemic in Cambodian ducks, and Eurasian low pathogenicity and high pathogenicity H5Nx AIVs. The detection of these H14 viruses in Southeast Asian domestic poultry further advances our knowledge of the ecology and evolution of this subtype and reinforces the need for continued, longitudinal, active surveillance in domestic and wild birds. Additionally, in vivo and in vitro risk assessment should encompass rare AIV subtypes, as they have the potential to establish in poultry systems.
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Affiliation(s)
- Jurre Y. Siegers
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Michelle Wille
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- WHO Collaborating Centre for Reference and Research on Influenza, at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Sokhoun Yann
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Songha Tok
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sarath Sin
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sokha Chea
- Wildlife Conservation Society, Phnom Penh, Cambodia
| | - Alice Porco
- Wildlife Conservation Society, Phnom Penh, Cambodia
| | - Sreyem Sours
- Wildlife Conservation Society, Phnom Penh, Cambodia
| | - Vutha Chim
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Samban Chea
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Kimtuo Chhel
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sothyra Tum
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - San Sorn
- National Animal Health and Production Research Institute, Phnom Penh, Cambodia
| | - Makara Hak
- Food and Agriculture Organization of the United Nations Country Office, Phnom Penh, Cambodia
| | - Peter Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, MD, USA
| | - Vijaykrishna Dhanasekaran
- School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, People’s Republic of China
- HKU-Pasteur Research Pole, School of Public Health, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, People’s Republic of China
| | - Erik A. Karlsson
- Virology Unit, Institute Pasteur du Cambodge, Phnom Penh, Cambodia
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Zhu W, Gu L. Resurgence of seasonal influenza driven by A/H3N2 and B/Victoria in succession during the 2023-2024 season in Beijing showing increased population susceptibility. J Med Virol 2024; 96:e29751. [PMID: 38884384 DOI: 10.1002/jmv.29751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/19/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
During the COVID-19 pandemic, non-pharmaceutical interventions were introduced to reduce exposure to respiratory viruses. However, these measures may have led to an "immunity debt" that could make the population more vulnerable. The goal of this study was to examine the transmission dynamics of seasonal influenza in the years 2023-2024. Respiratory samples from patients with influenza-like illness were collected and tested for influenza A and B viruses. The electronic medical records of index cases from October 2023 to March 2024 were analyzed to determine their clinical and epidemiological characteristics. A total of 48984 positive cases were detected, with a pooled prevalence of 46.9% (95% CI 46.3-47.5). This season saw bimodal peaks of influenza activity, with influenza A peaked in week 48, 2023, and influenza B peaked in week 1, 2024. The pooled positive rates were 28.6% (95% CI 55.4-59.6) and 18.3% (95% CI 18.0-18.7) for influenza A and B viruses, respectively. The median values of instantaneous reproduction number were 5.5 (IQR 3.0-6.7) and 4.6 (IQR 2.4-5.5), respectively. The hospitalization rate for influenza A virus (2.2%, 95% CI 2.0-2.5) was significantly higher than that of influenza B virus (1.1%, 95% CI 0.9-1.4). Among the 17 clinical symptoms studied, odds ratios of 15 symptoms were below 1 when comparing influenza A and B positive inpatients, with headache, weakness, and myalgia showing significant differences. This study provides an overview of influenza dynamics and clinical symptoms, highlighting the importance for individuals to receive an annual influenza vaccine.
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Affiliation(s)
- Wentao Zhu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
| | - Li Gu
- Department of Infectious Diseases and Clinical Microbiology, Beijing Institute of Respiratory Medicine and Beijing Chao-Yang Hospital, Capital Medical University, Beijing, P.R. China
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3
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Penteado AB, de Oliveira Ribeiro G, Lima Araújo EL, Kato RB, de Melo Freire CC, de Araújo JMG, da Luz Wallau G, Salvato RS, de Jesus R, Bosco GG, Franz HF, da Silva PEA, de Souza Leal E, Goulart Trossini GH, de Lima Neto DF. Binding Evolution of the Dengue Virus Envelope Against DC-SIGN: A Combined Approach of Phylogenetics and Molecular Dynamics Analyses Over 30 Years of Dengue Virus in Brazil. J Mol Biol 2024; 436:168577. [PMID: 38642883 DOI: 10.1016/j.jmb.2024.168577] [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: 01/09/2024] [Revised: 04/12/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
The Red Queen Hypothesis (RQH), derived from Lewis Carroll's "Through the Looking-Glass", postulates that organisms must continually adapt in response to each other to maintain relative fitness. Within the context of host-pathogen interactions, the RQH implies an evolutionary arms race, wherein viruses evolve to exploit hosts and hosts evolve to resist viral invasion. This study delves into the dynamics of the RQH in the context of virus-cell interactions, specifically focusing on virus receptors and cell receptors. We observed multiple virus-host systems and noted patterns of co-evolution. As viruses evolved receptor-binding proteins to effectively engage with cell receptors, cells countered by altering their receptor genes. This ongoing mutual adaptation cycle has influenced the molecular intricacies of receptor-ligand interactions. Our data supports the RQH as a driving force behind the diversification and specialization of both viral and host cell receptors. Understanding this co-evolutionary dance offers insights into the unpredictability of emerging viral diseases and potential therapeutic interventions. Future research is crucial to dissect the nuanced molecular changes and the broader ecological consequences of this ever-evolving battle. Here, we combine phylogenetic inferences, structural modeling, and molecular dynamics analyses to describe the epidemiological characteristics of major Brazilian DENV strains that circulated from 1990 to 2022 from a combined perspective, thus providing us with a more detailed picture on the dynamics of such interactions over time.
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MESH Headings
- Dengue Virus/genetics
- Dengue Virus/metabolism
- Receptors, Cell Surface/metabolism
- Receptors, Cell Surface/genetics
- Receptors, Cell Surface/chemistry
- Phylogeny
- Molecular Dynamics Simulation
- Humans
- Cell Adhesion Molecules/metabolism
- Cell Adhesion Molecules/genetics
- Cell Adhesion Molecules/chemistry
- Brazil
- Lectins, C-Type/metabolism
- Lectins, C-Type/genetics
- Lectins, C-Type/chemistry
- Evolution, Molecular
- Dengue/virology
- Host-Pathogen Interactions/genetics
- Protein Binding
- Viral Envelope/metabolism
- Receptors, Virus/metabolism
- Receptors, Virus/chemistry
- Receptors, Virus/genetics
- Viral Envelope Proteins/genetics
- Viral Envelope Proteins/metabolism
- Viral Envelope Proteins/chemistry
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Affiliation(s)
- André Berndt Penteado
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Geovani de Oliveira Ribeiro
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil; Department of Cellular Biology, University of Brasilia (UNB), Brasilia, Distrito Federal, Brazil
| | - Emerson Luiz Lima Araújo
- General Coordination of Attention to Communicable Diseases in Primary Care of the Department of Comprehensive Care Management of the Secretariat of Primary Health Care of the Ministry of Health (CDTAP/DGCI/SAPS-MS), Brazil
| | - Rodrigo Bentes Kato
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Caio Cesar de Melo Freire
- Department of Genetics and Evolution, Centre of Biological and Health Sciences, Federal University of Sao Carlos, PO Box 676, Washington Luis Road, km 235, São Carlos, SP 13565-905, Brazil
| | - Joselio Maria Galvão de Araújo
- Federal University of Rio Grande do Norte, Biosciences Center, Department of Microbiology and Parasitology, Campus Universitário, S/N Lagoa Nova 59078900, Natal, RN, Brazil
| | - Gabriel da Luz Wallau
- Department of Entomology and Bioinformatics Center of the Aggeu Magalhães Institute - FIOCRUZ - IAM, Brazil
| | - Richard Steiner Salvato
- Center for Scientific and Technological Development, State Center for Health Surveillance of Rio Grande do Sul, State Department of Health of Rio Grande do Sul, Porto Alegre, Brazil
| | - Ronaldo de Jesus
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Geraldine Goés Bosco
- University of São Paulo, Faculty of Philosophy Sciences and Letters of Ribeirão Preto. Av. Bandeirantes, 3900 Ribeirão Preto, SP, Brazil
| | - Helena Ferreira Franz
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Pedro Eduardo Almeida da Silva
- General-Coordination of Public Health Laboratories, Department of Strategic Coordination and Surveillance in Health and the Environment, Ministry of Health, Brasilia, Brazil
| | - Elcio de Souza Leal
- Federal University of Pará, Faculty of Biotechnology, Institute of Biological Sciences, Rua Augusto Corrêa, Guamá, 04039-032 Belem, PA, Brazil
| | - Gustavo Henrique Goulart Trossini
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil
| | - Daniel Ferreira de Lima Neto
- School of Pharmaceutical Sciences, University of São Paulo, Department of Pharmacy, Av. Prof. Lineu Prestes, 580, Cidade Universitária, São Paulo, SP 05508-000, Brazil.
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Zhirnov OP, Lvov DK. Avian flu: «for whom the bell tolls»? Vopr Virusol 2024; 69:101-118. [PMID: 38843017 DOI: 10.36233/10.36233/0507-4088-213] [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: 03/21/2024] [Indexed: 06/14/2024]
Abstract
The family Orthomyxoviridae consists of 9 genera, including Alphainfluenzavirus, which contains avian influenza viruses. In two subtypes H5 and H7 besides common low-virulent strains, a specific type of highly virulent avian virus have been described to cause more than 60% mortality among domestic birds. These variants of influenza virus are usually referred to as «avian influenza virus». The difference between high (HPAI) and low (LPAI) virulent influenza viruses is due to the structure of the arginine-containing proteolytic activation site in the hemagglutinin (HA) protein. The highly virulent avian influenza virus H5 was identified more than 100 years ago and during this time they cause outbreaks among wild and domestic birds on all continents and only a few local episodes of the disease in humans have been identified in XXI century. Currently, a sharp increase in the incidence of highly virulent virus of the H5N1 subtype (clade h2.3.4.4b) has been registered in birds on all continents, accompanied by the transmission of the virus to various species of mammals. The recorded global mortality rate among wild, domestic and agricultural birds from H5 subtype is approaching to the level of 1 billion cases. A dangerous epidemic factor is becoming more frequent outbreaks of avian influenza with high mortality among mammals, in particular seals and marine lions in North and South America, minks and fur-bearing animals in Spain and Finland, domestic and street cats in Poland. H5N1 avian influenza clade h2.3.4.4b strains isolated from mammals have genetic signatures of partial adaptation to the human body in the PB2, NP, HA, NA genes, which play a major role in regulating the aerosol transmission and the host range of the virus. The current situation poses a real threat of pre-adaptation of the virus in mammals as intermediate hosts, followed by the transition of the pre-adapted virus into the human population with catastrophic consequences.
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Affiliation(s)
- O P Zhirnov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
- The Russian-German Academy of Medical-Social and Biotechnological Sciences, Skolkovo Innovation Center
| | - D K Lvov
- The D.I. Ivaovsky Institute of Virology, The N.F. Gamaleya Research Center of Epidemiology and Microbiology, The Russian Ministry of Health
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Maya-Badillo BA, Orta-Pineda G, Zavala-Vasco D, Rivera-Rosas KE, Uribe-Jacinto A, Segura-Velásquez R, Suzán G, Sánchez-Betancourt JI. Influenza A virus antibodies in dogs, hunting dogs, and backyard pigs in Campeche, Mexico. Zoonoses Public Health 2024; 71:294-303. [PMID: 38196021 DOI: 10.1111/zph.13110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/16/2023] [Accepted: 12/26/2023] [Indexed: 01/11/2024]
Abstract
AIMS This study aimed to identify exposure to human, swine, and avian influenza A virus subtypes in rural companion and hunting dogs, backyard pigs, and feral pigs. METHODS AND RESULTS The study took place in a region of southeastern Mexico where the sampled individuals were part of backyard production systems in which different domestic and wild species coexist and interact with humans. We collected blood samples from pigs and dogs at each of the sites. We used a nucleoprotein enzyme-linked immunosorbent assay to determine the exposure of individuals to influenza A virus. Haemagglutination inhibition was performed on the positive samples to determine the subtypes to which they were exposed. For data analysis, a binomial logistic regression model was generated to determine the predictor variables for the seropositivity of the individuals in the study. We identified 11 positive individuals: three backyard pigs, four companion dogs, and four hunting dogs. The pigs tested positive for H1N1 and H1N2. The dogs were positive for H1N1, H1N2, and H3N2. The model showed that dogs in contact with backyard chickens are more likely to be seropositive for influenza A viruses. CONCLUSIONS We demonstrated the essential role hunting dogs could play as intermediate hosts and potential mixing vessel hosts when exposed to human and swine-origin viral subtypes. These results are relevant because these dogs interact with domestic hosts and humans in backyard systems, which are risk scenarios in the transmission of influenza A viruses. Therefore, it is of utmost importance to implement epidemiological surveillance of influenza A viruses in backyard animals, particularly in key animals in the transmission of these viruses, such as dogs and pigs.
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Affiliation(s)
- Brenda Aline Maya-Badillo
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
- Grupo de Investigación del Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Guillermo Orta-Pineda
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Diego Zavala-Vasco
- Grupo de Investigación del Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Karen Elizabeth Rivera-Rosas
- Grupo de Investigación del Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - René Segura-Velásquez
- Unidad de Investigación de la Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gerardo Suzán
- Laboratorio de Ecología de Enfermedades y Una Salud, Departamento de Fauna Silvestre y Animales de Laboratorio, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - José Iván Sánchez-Betancourt
- Grupo de Investigación del Departamento de Medicina y Zootecnia de Cerdos, Facultad de Medicina y Zootecnia, Universidad Nacional Autónoma de México, Mexico City, Mexico
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6
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Calhoun VC, Hatcher EL, Yankie L, Nawrocki EP. Influenza sequence validation and annotation using VADR. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.585980. [PMID: 38712272 PMCID: PMC11071281 DOI: 10.1101/2024.03.21.585980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
Tens of thousands of influenza sequences are deposited into the GenBank database each year. The software tool FLAN has been used by GenBank since 2007 to validate and annotate incoming influenza sequence submissions, and has been publicly available as a webserver but not as a standalone tool. VADR is a general sequence validation and annotation software package used by GenBank for Norovirus, Dengue virus and SARS-CoV-2 virus sequence processing that is available as a standalone tool. We have created VADR influenza models based on the FLAN reference sequences and adapted VADR to accurately annotate influenza sequences. VADR and FLAN show consistent results on the vast majority of influenza sequences, and when they disagree VADR is usually correct. VADR can also accurately process influenza D sequences as well as influenza A H17, H18, H19, N10 and N11 subtype sequences, which FLAN cannot. VADR 1.6.3 and the associated influenza models are now freely available for users to download and use.
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Affiliation(s)
- Vincent C. Calhoun
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, United States
| | - Eneida L. Hatcher
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, United States
| | - Linda Yankie
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, United States
| | - Eric P. Nawrocki
- National Center for Biotechnology Information, U.S. National Library of Medicine, National Institutes of Health, Bethesda, MD, 20894, United States
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7
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Chuang PH, Tzang BS, Tzang CC, Chiu CC, Lin CY, Hsu TC. Impact of oseltamivir on the risk of cancer. Front Oncol 2024; 14:1329986. [PMID: 38469236 PMCID: PMC10925756 DOI: 10.3389/fonc.2024.1329986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/26/2024] [Indexed: 03/13/2024] Open
Abstract
Purpose Mounting evidence has revealed the anti-cancer activity of various anti-viral drugs. Oseltamivir phosphate (OP), namely Tamiflu®, is routinely used to combat influenza infections. Although evidence has indicated the anti-cancer effects of OP in vitro and in vivo, little information is known about the effect of OP use on cancers in humans. Methods A nationwide population-based cohort study involving 13,977,101 cases with 284,733 receiving OP was performed to examine the association between OP use and cancers using the National Health Insurance Research Database in Taiwan between 2009 and 2018. Results The cohort study found that OP users showed a significantly lower incidence of lung cancer, colon cancer, liver, and intrahepatic bile duct cancer, oral cancer, pancreas cancer, esophagus cancer, stomach cancer, and prostate cancer. Additionally, OP users exhibited a lower risk of cancer-related mortality (adjusted HR=0.779; 95% confidence interval [CI] 0.743-0.817; p<0.001) and a reduced risk of developing liver cancer (adjusted HR=0.895; 95% CI 0.824-0.972; p=0.008), esophagus cancer (adjusted HR=0.646; 95% CI 0.522-0.799; p<0.001) and oral cancer (adjusted HR=0.587; 95% CI 0.346-0.995; p=0.048). Notably, OP users had a significant reduction in liver cancer occurrence over a 10-year period follow-up and a lower cancer stage at liver cancer diagnosis. Conclusion These findings first suggest the beneficial effects and therapeutic potential of OP use for certain cancers, especially liver cancer.
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Affiliation(s)
- Pei-Hua Chuang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Bor-Show Tzang
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Biochemistry, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
- Immunology Research Center, Chung Shan Medical University, Taichung, Taiwan
| | - Chih-Chen Tzang
- School of Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Chun-Ching Chiu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Neurology and Department of Medical Intensive Care Unit, Changhua Christian Hospital, Changhua, Taiwan
| | - Chun-Yu Lin
- Division of Allergy, Immunology, and Rheumatology, Department of Internal Medicine, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan
- School of Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Tsai-Ching Hsu
- Institute of Medicine, Chung Shan Medical University, Taichung, Taiwan
- Department of Clinical Laboratory, Chung Shan Medical University Hospital, Taichung, Taiwan
- Immunology Research Center, Chung Shan Medical University, Taichung, Taiwan
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8
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Kuchinski KS, Coombe M, Mansour SC, Cortez GAP, Kalhor M, Himsworth CG, Prystajecky NA. Targeted genomic sequencing of avian influenza viruses in wetland sediment from wild bird habitats. Appl Environ Microbiol 2024; 90:e0084223. [PMID: 38259077 PMCID: PMC10880596 DOI: 10.1128/aem.00842-23] [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: 05/23/2023] [Accepted: 11/30/2023] [Indexed: 01/24/2024] Open
Abstract
Diverse influenza A viruses (IAVs) circulate in wild birds, including highly pathogenic strains that infect poultry and humans. Consequently, surveillance of IAVs in wild birds is a cornerstone of agricultural biosecurity and pandemic preparedness. Surveillance is traditionally done by testing wild birds directly, but obtaining these specimens is labor intensive, detection rates can be low, and sampling is often biased toward certain avian species. As a result, local incursions of dangerous IAVs are rarely detected before outbreaks begin. Testing environmental specimens from wild bird habitats has been proposed as an alternative surveillance strategy. These specimens are thought to contain diverse IAVs deposited by a broad range of avian hosts, including species that are not typically sampled by surveillance programs. To enable this surveillance strategy, we developed a targeted genomic sequencing method for characterizing IAVs in these challenging environmental specimens. It combines custom hybridization probes, unique molecular index-based library construction, and purpose-built bioinformatic tools, allowing IAV genomic material to be enriched and analyzed with single-fragment resolution. We demonstrated our method on 90 sediment specimens from wetlands around Vancouver, Canada. We recovered 2,312 IAV genome fragments originating from all eight IAV genome segments. Eleven hemagglutinin subtypes and nine neuraminidase subtypes were detected, including H5, the current global surveillance priority. Our results demonstrate that targeted genomic sequencing of environmental specimens from wild bird habitats could become a valuable complement to avian influenza surveillance programs.IMPORTANCEIn this study, we developed genome sequencing tools for characterizing avian influenza viruses in sediment from wild bird habitats. These tools enable an environment-based approach to avian influenza surveillance. This could improve early detection of dangerous strains in local wild birds, allowing poultry producers to better protect their flocks and prevent human exposures to potential pandemic threats. Furthermore, we purposefully developed these methods to contend with viral genomic material that is diluted, fragmented, incomplete, and derived from multiple strains and hosts. These challenges are common to many environmental specimens, making these methods broadly applicable for genomic pathogen surveillance in diverse contexts.
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Affiliation(s)
- Kevin S. Kuchinski
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Michelle Coombe
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Sarah C. Mansour
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gabrielle Angelo P. Cortez
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marzieh Kalhor
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Chelsea G. Himsworth
- Animal Health Centre, Ministry of Agriculture and Food, Abbotsford, British Columbia, Canada
- School of Population and Public Health, University of British Columbia, Vancouver, British Columbia, Canada
- Canadian Wildlife Health Cooperative, Abbotsford, British Columbia, Canada
| | - Natalie A. Prystajecky
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- British Columbia Centre for Disease Control, Provincial Health Services Authority, Vancouver, British Columbia, Canada
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9
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Wen F, Wang C, Guo J, Yu H, Yuan S, Li Y, Li Z, Huang S, Liang Z. Development and application of a triplex real-time PCR assay for the detection of H3, H4, and H5 subtypes of avian influenza virus. Poult Sci 2024; 103:103333. [PMID: 38113705 PMCID: PMC10770746 DOI: 10.1016/j.psj.2023.103333] [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: 09/18/2023] [Revised: 11/24/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023] Open
Abstract
Avian influenza virus (AIV) poses a significant threat to the poultry industry and public health. Among the diverse AIV subtypes, H3, H4, and H5 are frequently detected in waterfowl and live poultry markets (LPM). The expeditious and precise identification of these subtypes is imperative in impeding the dissemination of the disease. In this study, we have developed a triplex real-time PCR assay endowed with the capacity to simultaneously discriminate AIV subtypes H3, H4, and H5. This method showcases remarkable specificity, selectively amplifying H3, H4, and H5 AIV subtypes sans any cross-reactivity with other subtypes or common avian pathogens. Furthermore, this method exhibits high sensitivity, with a detection threshold of 2.1 × 102 copies/μL for H3, H4, and H5 AIV subtypes. Additionally, the assay demonstrates reproducibility, as evidenced by intra- and interassay variability, with a coefficient of variation below 1.5%. A total of 338 cloacal swabs were collected from LPM to evaluate the performance of our assay. The obtained results evinced a high level of concordance with the sequencing data. In summary, our study has developed a triplex real-time PCR method that can be employed in laboratory-based testing and surveillance of AIV. This assay holds promise in augmenting our ability to detect and monitor AIV subtypes, thereby facilitating timely interventions and safeguarding both the poultry industry and public health.
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Affiliation(s)
- Feng Wen
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Congying Wang
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Jinyue Guo
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Hai Yu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Sheng Yuan
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Yong Li
- College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang 330045, Jiangxi, China
| | - Zhili Li
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Shujian Huang
- College of Life Science and Engineering, Foshan University, Foshan 528231, Guangdong, China
| | - Zhaoping Liang
- College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, Guangdong, China.
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10
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Li X, Li Y, Shang X, Kong H. A sequence-based machine learning model for predicting antigenic distance for H3N2 influenza virus. Front Microbiol 2024; 15:1345794. [PMID: 38314434 PMCID: PMC10834737 DOI: 10.3389/fmicb.2024.1345794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Introduction Seasonal influenza A H3N2 viruses are constantly changing, reducing the effectiveness of existing vaccines. As a result, the World Health Organization (WHO) needs to frequently update the vaccine strains to match the antigenicity of emerged H3N2 variants. Traditional assessments of antigenicity rely on serological methods, which are both labor-intensive and time-consuming. Although numerous computational models aim to simplify antigenicity determination, they either lack a robust quantitative linkage between antigenicity and viral sequences or focus restrictively on selected features. Methods Here, we propose a novel computational method to predict antigenic distances using multiple features, including not only viral sequence attributes but also integrating four distinct categories of features that significantly affect viral antigenicity in sequences. Results This method exhibits low error in virus antigenicity prediction and achieves superior accuracy in discerning antigenic drift. Utilizing this method, we investigated the evolution process of the H3N2 influenza viruses and identified a total of 21 major antigenic clusters from 1968 to 2022. Discussion Interestingly, our predicted antigenic map aligns closely with the antigenic map generated with serological data. Thus, our method is a promising tool for detecting antigenic variants and guiding the selection of vaccine candidates.
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Affiliation(s)
- Xingyi Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Yanyan Li
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Xuequn Shang
- School of Computer Science, Northwestern Polytechnical University, Xi'an, Shaanxi, China
- Big Data Storage and Management MIIT Lab, Xi'an, Shaanxi, China
| | - Huihui Kong
- State Key Laboratory of Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
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11
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Zhu M, Zeng H, He J, Zhu Y, Wang P, Guo J, Guo J, Zhou H, Qin Y, Ouyang K, Wei Z, Huang W, Chen Y. Reassortant H9N2 canine influenza viruses containing the pandemic H1N1/2009 ribonucleoprotein complex circulating in pigs acquired enhanced virulence in mice. Virology 2024; 589:109927. [PMID: 37951087 DOI: 10.1016/j.virol.2023.109927] [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: 07/26/2023] [Revised: 10/08/2023] [Accepted: 10/30/2023] [Indexed: 11/13/2023]
Abstract
The reassortment between avian H9N2 and Eurasian avian-like (EA) H1N1 viruses may have potentially changed from avian-to-mammals adaptation. This study generated 20 reassortant viruses with the introduction of H1N1/2009 internal genes from EA H1N1 virus into H9N2 virus. 12 of these recovered the replication capability both in the lungs and turbinate samples. 10 of 12 obtained PA gene segments from the ribonucleoprotein (RNP) complexes of the EA H1N1 virus, and 3 exhibited extreme virulence. Specially, the combination of PB2, PA and NP genes could overcome the species-specific restriction in human cells. Analysis of the polymerase activities found that introduction of the PA gene resulted in increased polymerase activity. These findings indicated that RNP complexes from EA H1N1 virus could confer an adaptation advantage and high compatibility to avian H9N2 virus. This raises new concerns for public health due to the possible coexistence of H9N2 and EA H1N1 viruses in dogs.
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Affiliation(s)
- Min Zhu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Hao Zeng
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Jianqiao He
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Yaohui Zhu
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Pingping Wang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Jianing Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Jinfan Guo
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China
| | - Huabo Zhou
- Huabo Pet Hospital, Nanning, 530004, PR China
| | - Yifeng Qin
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Kang Ouyang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Zuzhang Wei
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Weijian Huang
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China
| | - Ying Chen
- Laboratory of Animal Infectious Diseases and Molecular Immunology, College of Animal Science and Technology, Guangxi University, Nanning, 530004, PR China; Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning, 530004, PR China; Guangxi Key Laboratory of Animal Breeding, Disease Prevention and Control, Nanning, 530004, PR China; Guangxi College and Universities Key Laboratory of Prevention and Control for Animal Disease, Nanning, 530004, PR China.
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12
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Matevosyan M, Harutyunyan V, Abelyan N, Khachatryan H, Tirosyan I, Gabrielyan Y, Sahakyan V, Gevorgyan S, Arakelov V, Arakelov G, Zakaryan H. Design of new chemical entities targeting both native and H275Y mutant influenza a virus by deep reinforcement learning. J Biomol Struct Dyn 2023; 41:10798-10812. [PMID: 36541127 DOI: 10.1080/07391102.2022.2158936] [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: 08/02/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Influenza virus remains a major public health challenge due to its high morbidity and mortality and seasonal surge. Although antiviral drugs against the influenza virus are widely used as a first-line defense, the virus undergoes rapid genetic changes, resulting in the emergence of drug-resistant strains. Thus, new antiviral drugs that can outwit resistant strains are of significant importance. Herein, we used deep reinforcement learning (RL) algorithm to design new chemical entities (NCEs) that are able to bind to the native and H275Y mutant (oseltamivir-resistant) neuraminidases (NAs) of influenza A virus with better binding energy than oseltamivir. We generated more than 66211 NCEs, which were prioritized based on the filtering rules, structural alerts, and synthetic accessibility. Then, 18 NCEs with better MM/PBSA scores than oseltamivir were further analyzed in molecular dynamics (MD) simulations conducted for 100 ns. The MD experiments showed that 8 NCEs formed very stable complexes with the binding pocket of both native and H275Y mutant NAs of H1N1. Furthermore, most NCEs demonstrated much better binding affinity to group 2 (N2, N3, and N9) and influenza B virus NAs than oseltamivir. Although all 8 NCEs have non-sialic acid-like structures, they showed a similar binding mode as oseltamivir, indicating that it is possible to find new scaffolds with better binding and antiviral properties than sialic acid-like inhibitors. In conclusion, we have designed potential compounds as antiviral candidates for further synthesis and testing against wild and mutant influenza virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Vahram Arakelov
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
| | - Grigor Arakelov
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
| | - Hovakim Zakaryan
- Denovo Sciences Inc, Yerevan, Armenia
- Institute of Molecular Biology of National Academy of Sciences, Yerevan, Armenia
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13
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Rak A, Isakova-Sivak I, Rudenko L. Nucleoprotein as a Promising Antigen for Broadly Protective Influenza Vaccines. Vaccines (Basel) 2023; 11:1747. [PMID: 38140152 PMCID: PMC10747533 DOI: 10.3390/vaccines11121747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 11/17/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Annual vaccination is considered as the main preventive strategy against seasonal influenza. Due to the highly variable nature of major viral antigens, such as hemagglutinin (HA) and neuraminidase (NA), influenza vaccine strains should be regularly updated to antigenically match the circulating viruses. The influenza virus nucleoprotein (NP) is much more conserved than HA and NA, and thus seems to be a promising target for the design of improved influenza vaccines with broad cross-reactivity against antigenically diverse influenza viruses. Traditional subunit or recombinant protein influenza vaccines do not contain the NP antigen, whereas live-attenuated influenza vaccines (LAIVs) express the viral NP within infected cells, thus inducing strong NP-specific antibodies and T-cell responses. Many strategies have been explored to design broadly protective NP-based vaccines, mostly targeted at the T-cell mode of immunity. Although the NP is highly conserved, it still undergoes slow evolutionary changes due to selective immune pressure, meaning that the particular NP antigen selected for vaccine design may have a significant impact on the overall immunogenicity and efficacy of the vaccine candidate. In this review, we summarize existing data on the conservation of the influenza A viral nucleoprotein and review the results of preclinical and clinical trials of NP-targeting influenza vaccine prototypes, focusing on the ability of NP-specific immune responses to protect against diverse influenza viruses.
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Affiliation(s)
| | | | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, St. Petersburg 197022, Russia; (A.R.); (I.I.-S.)
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14
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Petrone ME, Parry R, Mifsud JCO, Van Brussel K, Vorhees I, Richards ZT, Holmes EC. Evidence for an ancient aquatic origin of the RNA viral order Articulavirales. Proc Natl Acad Sci U S A 2023; 120:e2310529120. [PMID: 37906647 PMCID: PMC10636315 DOI: 10.1073/pnas.2310529120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/03/2023] [Indexed: 11/02/2023] Open
Abstract
The emergence of previously unknown disease-causing viruses in mammals is in part the result of a long-term evolutionary process. Reconstructing the deep phylogenetic histories of viruses helps identify major evolutionary transitions and contextualizes the emergence of viruses in new hosts. We used a combination of total RNA sequencing and transcriptome data mining to extend the diversity and evolutionary history of the RNA virus order Articulavirales, which includes the influenza viruses. We identified instances of Articulavirales in the invertebrate phylum Cnidaria (including corals), constituting a novel and divergent family that we provisionally named the "Cnidenomoviridae." We further extended the evolutionary history of the influenza virus lineage by identifying four divergent, fish-associated influenza-like viruses, thereby supporting the hypothesis that fish were among the first hosts of influenza viruses. In addition, we substantially expanded the phylogenetic diversity of quaranjaviruses and proposed that this genus be reclassified as a family-the "Quaranjaviridae." Within this putative family, we identified a novel arachnid-infecting genus, provisionally named "Cheliceravirus." Notably, we observed a close phylogenetic relationship between the Crustacea- and Chelicerata-infecting "Quaranjaviridae" that is inconsistent with virus-host codivergence. Together, these data suggest that the Articulavirales has evolved over at least 600 million years, first emerging in aquatic animals. Importantly, the evolution of the Articulavirales was likely shaped by multiple aquatic-terrestrial transitions and substantial host jumps, some of which are still observable today.
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Affiliation(s)
- Mary E. Petrone
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
| | - Rhys Parry
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD4067, Australia
| | - Jonathon C. O. Mifsud
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Kate Van Brussel
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
| | - Ian Vorhees
- James A. Baker Institute for Animal Health, Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY14850
| | - Zoe T. Richards
- Coral Conservation and Research Group, Trace and Environmental DNA Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA6102, Australia
- Collections and Research, Western Australian Museum, Welshpool, WA6106, Australia
| | - Edward C. Holmes
- Sydney Institute for Infectious Diseases, School of Medical Sciences, The University of Sydney, Sydney, NSW2006, Australia
- Laboratory of Data Discovery for Health Limited, Hong Kong Special Administrative Region, China
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15
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Godoy M, de Oca MM, Caro D, Pontigo JP, Kibenge M, Kibenge F. Evolution and Current Status of Influenza A Virus in Chile: A Review. Pathogens 2023; 12:1252. [PMID: 37887768 PMCID: PMC10610240 DOI: 10.3390/pathogens12101252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/28/2023] Open
Abstract
The influenza A virus (IAV) poses a significant global threat to public health and food security. Particularly concerning is the avian influenza virus (AIV) subtype H5N1, which has spread from Europe to North and Central/South America. This review presents recent developments in IAV evolution in birds, mammals, and humans in Chile. Chile's encounter with IAV began in 2002, with the highly pathogenic avian influenza (HPAI) H7N3 virus, derived from a unique South American low pathogenic avian influenza (LPAI) virus. In 2016-2017, LPAI H7N6 caused outbreaks in turkey, linked to wild birds in Chile and Bolivia. The pandemic influenza A (H1N1) 2009 (H1N1pdm09) virus in 2009 decreased egg production in turkeys. Since 2012, diverse IAV subtypes have emerged in backyard poultry and pigs. Reassortant AIVs, incorporating genes from both North and South American isolates, have been found in wild birds since 2007. Notably, from December 2022, HPAI H5N1 was detected in wild birds, sea lions, and a human, along Chile's north coast. It was introduced through Atlantic migratory flyways from North America. These findings emphasize the need for enhanced biosecurity on poultry farms and ongoing genomic surveillance to understand and manage AIVs in both wild and domestic bird populations in Chile.
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Affiliation(s)
- Marcos Godoy
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5480000, Chile; (M.M.d.O.); (D.C.)
- Laboratorio de Biotecnología Aplicada, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Sede de la Patagonia, Universidad San Sebastián, Puerto Montt 5480000, Chile;
| | - Marco Montes de Oca
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5480000, Chile; (M.M.d.O.); (D.C.)
| | - Diego Caro
- Centro de Investigaciones Biológicas Aplicadas (CIBA), Puerto Montt 5480000, Chile; (M.M.d.O.); (D.C.)
| | - Juan Pablo Pontigo
- Laboratorio de Biotecnología Aplicada, Facultad de Ciencias de la Naturaleza, Escuela de Medicina Veterinaria, Sede de la Patagonia, Universidad San Sebastián, Puerto Montt 5480000, Chile;
| | - Molly Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE C1A 4P3, Canada;
| | - Frederick Kibenge
- Department of Pathology and Microbiology, Atlantic Veterinary College, University of Prince Edward Island, 550 University Ave, Charlottetown, PE C1A 4P3, Canada;
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16
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Carnegie L, Raghwani J, Fournié G, Hill SC. Phylodynamic approaches to studying avian influenza virus. Avian Pathol 2023; 52:289-308. [PMID: 37565466 DOI: 10.1080/03079457.2023.2236568] [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: 02/02/2023] [Revised: 06/23/2023] [Accepted: 07/07/2023] [Indexed: 08/12/2023]
Abstract
Avian influenza viruses can cause severe disease in domestic and wild birds and are a pandemic threat. Phylodynamics is the study of how epidemiological, evolutionary, and immunological processes can interact to shape viral phylogenies. This review summarizes how phylodynamic methods have and could contribute to the study of avian influenza viruses. Specifically, we assess how phylodynamics can be used to examine viral spread within and between wild or domestic bird populations at various geographical scales, identify factors associated with virus dispersal, and determine the order and timing of virus lineage movement between geographic regions or poultry production systems. We discuss factors that can complicate the interpretation of phylodynamic results and identify how future methodological developments could contribute to improved control of the virus.
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Affiliation(s)
- L Carnegie
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - J Raghwani
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
| | - G Fournié
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
- Université de Lyon, INRAE, VetAgro Sup, UMR EPIA, Marcy l'Etoile, France
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint Genes Champanelle, France
| | - S C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College (RVC), Hatfield, UK
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17
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Cui P, Shi J, Yan C, Wang C, Zhang Y, Zhang Y, Xing X, Chen Y, Zhang J, Liu L, Zeng X, Tian G, Li C, Suzuki Y, Deng G, Chen H. Analysis of avian influenza A (H3N8) viruses in poultry and their zoonotic potential, China, September 2021 to May 2022. Euro Surveill 2023; 28:2200871. [PMID: 37824247 PMCID: PMC10571489 DOI: 10.2807/1560-7917.es.2023.28.41.2200871] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 04/14/2023] [Indexed: 10/14/2023] Open
Abstract
BackgroundTwo human cases of avian influenza A (H3N8) virus infection were reported in China in 2022.AimTo characterise H3N8 viruses circulating in China in September 2021-May 2022.MethodsWe sampled poultry and poultry-related environments in 25 Chinese provinces. After isolating H3N8 viruses, whole genome sequences were obtained for molecular and phylogenetic analyses. The specificity of H3N8 viruses towards human or avian receptors was assessed in vitro. Their ability to replicate in chicken and mice, and to transmit between guinea pigs was also investigated.ResultsIn total, 98 H3N8 avian influenza virus isolates were retrieved from 38,639 samples; genetic analysis of 31 representative isolates revealed 17 genotypes. Viruses belonging to 10 of these genotypes had six internal genes originating from influenza A (H9N2) viruses. These reassorted viruses could be found in live poultry markets and comprised the strains responsible for the two human infections. A subset of nine H3N8 viruses (including six reassorted) that replicated efficiently in mice bound to both avian-type and human-type receptors in vitro. Three reassorted viruses were shed by chickens for up to 9 days, replicating efficiently in their upper respiratory tract. Five reassorted viruses tested on guinea pigs were transmissible among these by respiratory droplets.ConclusionAvian H3N8 viruses with H9N2 virus internal genes, causing two human infections, occurred in live poultry markets in China. The low pathogenicity of H3N8 viruses in poultry allows their continuous circulation with potential for reassortment. Careful monitoring of spill-over infections in humans is important to strengthen early-warning systems and maintain influenza pandemic preparedness.
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Affiliation(s)
- Pengfei Cui
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
- National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, CAAS, Harbin, China
- These authors contributed equally to this manuscript
| | - Jianzhong Shi
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
- National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, CAAS, Harbin, China
- These authors contributed equally to this manuscript
- Western Research Institute, CAAS, Changji, China
| | - Cheng Yan
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
- These authors contributed equally to this manuscript
| | - Congcong Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yuancheng Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yaping Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Xin Xing
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yuan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Jie Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Liling Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Xianying Zeng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Guobin Tian
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Chengjun Li
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yasuo Suzuki
- Department of Medical Biochemistry, University of Shizuoka School of Pharmaceutical Sciences, Shizuoka, Japan
| | - Guohua Deng
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Hualan Chen
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, CAAS, Harbin, China
- National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, CAAS, Harbin, China
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18
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Szaluś-Jordanow O, Golke A, Dzieciątkowski T, Chrobak-Chmiel D, Rzewuska M, Czopowicz M, Sapierzyński R, Kardas M, Biernacka K, Mickiewicz M, Moroz-Fik A, Łobaczewski A, Stefańska I, Kwiecień E, Markowska-Daniel I, Frymus T. A Fatal A/H5N1 Avian Influenza Virus Infection in a Cat in Poland. Microorganisms 2023; 11:2263. [PMID: 37764107 PMCID: PMC10538095 DOI: 10.3390/microorganisms11092263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/27/2023] [Accepted: 09/07/2023] [Indexed: 09/29/2023] Open
Abstract
A European Shorthair male cat, neutered, approximately 6 years of age, was presented to the veterinary clinic due to apathy and anorexia. The cat lived mostly outdoors and was fed raw chicken meat. After 3 days of diagnostic procedures and symptomatic treatment, respiratory distress and neurological signs developed and progressed into epileptic seizures, followed by respiratory and cardiac arrest within the next 3 days. Post-mortem examination revealed necrotic lesions in the liver, lungs, and intestines. Notably, the brain displayed perivascular infiltration of lymphocytes and histiocytes. Few foci of neuronal necrosis in the brain were also confirmed. Microscopic examination of the remaining internal organs was unremarkable. The A/H5N1 virus infection was confirmed using a one-step real-time reverse transcription polymerase chain reaction (RT-qPCR). The disease caused severe neurological and respiratory signs, evidence of consolidations and the presence of numerous B lines, which were detected on lung ultrasound examination; the postmortem findings and detection of A/H5N1 viral RNA in multiple tissues indicated a generalized A/H5N1 virus infection. Moreover, a multidrug-resistant strain of Enterococcus faecium was isolated in pure culture from several internal organs. The source of infection could be exposure to infected birds or their excrements, as well as contaminated raw poultry meat but, in this case, the source of infection could not be identified.
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Affiliation(s)
- Olga Szaluś-Jordanow
- Department of Small Animal Diseases with Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Anna Golke
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Tomasz Dzieciątkowski
- Chair and Department of Medical Microbiology, Medical University of Warsaw, Chałubińskiego 5, 02-004 Warsaw, Poland
| | - Dorota Chrobak-Chmiel
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Magdalena Rzewuska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Michał Czopowicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Rafał Sapierzyński
- Department of Pathology and Veterinary Diagnostics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Michał Kardas
- Veterinary Clinic Auxilium, Arkadiusz Olkowski, Królewska Str. 64, 05-822 Milanówek, Poland
| | - Kinga Biernacka
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Marcin Mickiewicz
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Agata Moroz-Fik
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Andrzej Łobaczewski
- Veterinary Clinic Auxilium, Arkadiusz Olkowski, Królewska Str. 64, 05-822 Milanówek, Poland
| | - Ilona Stefańska
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Ewelina Kwiecień
- Department of Preclinical Sciences, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Ciszewskiego 8, 02-786 Warsaw, Poland
| | - Iwona Markowska-Daniel
- Division of Veterinary Epidemiology and Economics, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
| | - Tadeusz Frymus
- Department of Small Animal Diseases with Clinic, Institute of Veterinary Medicine, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159c, 02-776 Warsaw, Poland
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Pereira PDC, Diniz DG, da Costa ER, Magalhães NGDM, da Silva ADJF, Leite JGS, Almeida NIP, Cunha KDN, de Melo MAD, Vasconcelos PFDC, Diniz JAP, Brites D, Anthony DC, Diniz CWP, Guerreiro-Diniz C. Genes, inflammatory response, tolerance, and resistance to virus infections in migratory birds, bats, and rodents. Front Immunol 2023; 14:1239572. [PMID: 37711609 PMCID: PMC10497949 DOI: 10.3389/fimmu.2023.1239572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 08/14/2023] [Indexed: 09/16/2023] Open
Abstract
Normally, the host immunological response to viral infection is coordinated to restore homeostasis and protect the individual from possible tissue damage. The two major approaches are adopted by the host to deal with the pathogen: resistance or tolerance. The nature of the responses often differs between species and between individuals of the same species. Resistance includes innate and adaptive immune responses to control virus replication. Disease tolerance relies on the immune response allowing the coexistence of infections in the host with minimal or no clinical signs, while maintaining sufficient viral replication for transmission. Here, we compared the virome of bats, rodents and migratory birds and the molecular mechanisms underlying symptomatic and asymptomatic disease progression. We also explore the influence of the host physiology and environmental influences on RNA virus expression and how it impacts on the whole brain transcriptome of seemingly healthy semipalmated sandpiper (Calidris pusilla) and spotted sandpiper (Actitis macularius). Three time points throughout the year were selected to understand the importance of longitudinal surveys in the characterization of the virome. We finally revisited evidence that upstream and downstream regulation of the inflammatory response is, respectively, associated with resistance and tolerance to viral infections.
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Affiliation(s)
- Patrick Douglas Corrêa Pereira
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Daniel Guerreiro Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Emanuel Ramos da Costa
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Nara Gyzely de Morais Magalhães
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Anderson de Jesus Falcão da Silva
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Jéssica Gizele Sousa Leite
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Natan Ibraim Pires Almeida
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Kelle de Nazaré Cunha
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Mauro André Damasceno de Melo
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
| | - Pedro Fernando da Costa Vasconcelos
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Pará, Brazil
- Seção de Arbovirologia e Febres Hemorrágicas, Instituto Evandro Chagas, Ananindeua, Pará, Brazil
| | - José Antonio Picanço Diniz
- Seção de Hepatologia, Laboratório de Microscopia Eletrônica, Instituto Evandro Chagas, Belém, Pará, Brazil
| | - Dora Brites
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Department of Pharmaceutical Sciences and Medicines, Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Daniel Clive Anthony
- Department of Pharmacology, Laboratory of Experimental Neuropathology, University of Oxford, Oxford, United Kingdom
| | - Cristovam Wanderley Picanço Diniz
- Instituto de Ciências Biológicas, Hospital Universitário João de Barros Barreto, Laboratório de Investigações em Neurodegeneração e Infecção, Universidade Federal do Pará, Belém, Pará, Brazil
| | - Cristovam Guerreiro-Diniz
- Ciência e Tecnologia do Pará, Laboratório de Biologia Molecular e Neuroecologia, Instituto Federal de Educação, Bragança, Pará, Brazil
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20
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Yao Y, Zou M, Wu H, Ma S, Gu X, Zhou M, Zhao F, Abudushalamua G, Xiao F, Chen Y, Cai S, Fan X, Wu G. A colloidal gold test strip based on catalytic hairpin assembly for the clinical detection of influenza a virus nucleic acid. Talanta 2023; 265:124855. [PMID: 37406394 DOI: 10.1016/j.talanta.2023.124855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Revised: 06/11/2023] [Accepted: 06/20/2023] [Indexed: 07/07/2023]
Abstract
Influenza A epidemics, which occur annually in varying degrees worldwide, is a global challenge to healthcare facilities owing to several limitations of the current detection methods. Therefore, the development of a rapid, convenient, and economical method for the early diagnosis of influenza A will aid clinical treatment and epidemic control. Currently, most of the commonly used clinical rapid tests utilize colloidal gold test strips that detect specific influenza virus antigens but are limited by low sensitivity. Therefore, this study combined catalytic hairpin assembly (CHA) with colloidal gold immunochromatographic assay (GICA) to develop a highly sensitive and visual CHA-GICA test strip. Clinical sample analysis revealed that the sensitivity of the assay was 81.8% and 74% under optimal (35 °C) and room temperature (25 °C) conditions, respectively. In conclusion, this study developed a rapid nucleic acid assay for detecting influenza A virus with high sensitivity and specificity, which can improve the clinical detection of influenza A.
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Affiliation(s)
- Yuming Yao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Mingyuan Zou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Huina Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Shuo Ma
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Xiaoyu Gu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Meiling Zhou
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Fengfeng Zhao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Gulinazhaer Abudushalamua
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Feng Xiao
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Yaya Chen
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Shijie Cai
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China
| | - Xiaobo Fan
- Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China.
| | - Guoqiu Wu
- Center of Clinical Laboratory Medicine, Zhongda Hospital, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Department of Laboratory Medicine, Medical School of Southeast University, Nanjing, 210009, Jiangsu, China; Jiangsu Provincial Key Laboratory of Critical Care Medicine, Southeast University, Nanjing, 210009, Jiangsu, China.
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21
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Niu J, Meng G. Roles and Mechanisms of NLRP3 in Influenza Viral Infection. Viruses 2023; 15:1339. [PMID: 37376638 DOI: 10.3390/v15061339] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/05/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Pathogenic viral infection represents a major challenge to human health. Due to the vast mucosal surface of respiratory tract exposed to the environment, host defense against influenza viruses has perpetually been a considerable challenge. Inflammasomes serve as vital components of the host innate immune system and play a crucial role in responding to viral infections. To cope with influenza viral infection, the host employs inflammasomes and symbiotic microbiota to confer effective protection at the mucosal surface in the lungs. This review article aims to summarize the current findings on the function of NACHT, LRR and PYD domains-containing protein 3 (NLRP3) in host response to influenza viral infection involving various mechanisms including the gut-lung crosstalk.
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Affiliation(s)
- Junling Niu
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, University of Chinese Academy of Sciences, 320 Yueyang Road, Life Science Research Building B-205, Shanghai 200031, China
| | - Guangxun Meng
- The Center for Microbes, Development and Health, CAS Key Laboratory of Molecular Virology & Immunology, University of Chinese Academy of Sciences, 320 Yueyang Road, Life Science Research Building B-205, Shanghai 200031, China
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22
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Zeng H, Cai M, Li S, Chen X, Xu X, Xie W, Xiong Y, Long X. Epidemiological characteristics of seasonal influenza under implementation of zero-COVID-19 strategy in China. J Infect Public Health 2023; 16:1158-1166. [PMID: 37269694 DOI: 10.1016/j.jiph.2023.05.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Revised: 03/23/2023] [Accepted: 05/10/2023] [Indexed: 06/05/2023] Open
Abstract
OBJECTIVE Respiratory viral diseases have posed a persistent threat to public health due to their high transmissibility. Influenza virus and SARS-Cov-2 are both respiratory viruses that have caused global pandemics. A zero-COVID-19 strategy is a public health policy imposed to stop community transmission of COVID-19 as soon as it is detected. In this study, we aim to examine the epidemiological characteristics of seasonal influenza in the past five years before and after the emergence of COVID-19 in China and observe the possible impact of the strategy on influenza. METHODS Data from two data sources were retrospectively analyzed. A comparison on influenza incidence rate between Hubei and Zhejiang provinces was conducted based on data from the Chinese Center for Disease Control and Prevention (CDC). Then a descriptive and comparative analysis on seasonal influenza based on data from Zhongnan Hospital of Wuhan University and Hangzhou Ninth People`s Hospital before and after the outbreak of SARS-CoV-2 was conducted. RESULTS From 2010-2017, both provinces experienced relatively low influenza activity until the 1st week of 2018, when they reached peak incidence rates of 78.16/100000PY, 34.05/100000PY respectively. Since then, influenza showed an obvious seasonality in Hubei and Zhejiang until the onset of COVID-19. During 2020 and 2021, there was a dramatic decline in influenza activity compared to 2018 and 2019. However, influenza activity seemed to rebound at the beginning of 2022 and surged in summer, with positive rates of 20.52% and 31.53% in Zhongnan Hospital of Wuhan University and Hangzhou Ninth People`s Hospital respectively as of the time writing this article. CONCLUSIONS Our results reinforce the hypothesis that zero-COVID-19 strategy may impact the epidemiological pattern of influenza. Under the complex pandemic situation, implementation of NPIs could be a beneficial strategy containing not only COVID-19 but also influenza.
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Affiliation(s)
- Hui Zeng
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China; Center of Clinical Laboratory, Hangzhou Ninth People's Hospital, Hangzhou, China
| | - Meihong Cai
- Department of Dermatology,Wuhan Wuchang Hospital, Wuchang Hospital Affiliated to Wuhan University of Science and Technology, Wuhan, China
| | - Shiqi Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiaoping Chen
- Department of infectious diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xianqun Xu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Wen Xie
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yong Xiong
- Department of infectious diseases, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xinghua Long
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
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23
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Rasmussen EA, Czaja A, Cuthbert FJ, Tan GS, Lemey P, Nelson MI, Culhane MR. Influenza A viruses in gulls in landfills and freshwater habitats in Minnesota, United States. Front Genet 2023; 14:1172048. [PMID: 37229191 PMCID: PMC10203411 DOI: 10.3389/fgene.2023.1172048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 04/10/2023] [Indexed: 05/27/2023] Open
Abstract
Introduction: The unpredictable evolution of avian influenza viruses (AIVs) presents an ongoing threat to agricultural production and public and wildlife health. Severe outbreaks of highly pathogenic H5N1 viruses in US poultry and wild birds since 2022 highlight the urgent need to understand the changing ecology of AIV. Surveillance of gulls in marine coastal environments has intensified in recent years to learn how their long-range pelagic movements potentially facilitate inter-hemispheric AIV movements. In contrast, little is known about inland gulls and their role in AIV spillover, maintenance, and long-range dissemination. Methods: To address this gap, we conducted active AIV surveillance in ring-billed gulls (Larus delawarensis) and Franklin's gulls (Leucophaeus pipixcan) in Minnesota's natural freshwater lakes during the summer breeding season and in landfills during fall migration (1,686 samples). Results: Whole-genome AIV sequences obtained from 40 individuals revealed three-lineage reassortants with a mix of genome segments from the avian Americas lineage, avian Eurasian lineage, and a global "Gull" lineage that diverged more than 50 years ago from the rest of the AIV global gene pool. No poultry viruses contained gull-adapted H13, NP, or NS genes, pointing to limited spillover. Geolocators traced gull migration routes across multiple North American flyways, explaining how inland gulls imported diverse AIV lineages from distant locations. Migration patterns were highly varied and deviated far from assumed "textbook" routes. Discussion: Viruses circulating in Minnesota gulls during the summer breeding season in freshwater environments reappeared in autumn landfills, evidence of AIV persistence in gulls between seasons and transmission between habitats. Going forward, wider adoption of technological advances in animal tracking devices and genetic sequencing is needed to expand AIV surveillance in understudied hosts and habitats.
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Affiliation(s)
- Elizabeth A. Rasmussen
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
| | - Agata Czaja
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Francesca J. Cuthbert
- Department of Fisheries, Wildlife and Conservation Biology, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Minneapolis, MN, United States
| | - Gene S. Tan
- J. Craig Venter Institute, La Jolla, Division of Infectious Diseases, Department of Medicine, University of California San Diego, La Jolla, CA, United States
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Martha I. Nelson
- Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Marie R. Culhane
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, Saint Paul, MN, United States
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24
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Crespo-Bellido A, Duffy S. The how of counter-defense: viral evolution to combat host immunity. Curr Opin Microbiol 2023; 74:102320. [PMID: 37075547 DOI: 10.1016/j.mib.2023.102320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Viruses are locked in an evolutionary arms race with their hosts. What ultimately determines viral evolvability, or capacity for adaptive evolution, is their ability to efficiently explore and expand sequence space while under the selective regime imposed by their ecology, which includes innate and adaptive host defenses. Viral genomes have significantly higher evolutionary rates than their host counterparts and should have advantages relative to their slower-evolving hosts. However, functional constraints on virus evolutionary landscapes along with the modularity and mutational tolerance of host defense proteins may help offset the advantage conferred to viruses by high evolutionary rates. Additionally, cellular life forms from all domains of life possess many highly complex defense mechanisms that act as hurdles to viral replication. Consequently, viruses constantly probe sequence space through mutation and genetic exchange and are under pressure to optimize diverse counter-defense strategies.
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Affiliation(s)
- Alvin Crespo-Bellido
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers, the State University of New Jersey, New Brunswick, NJ, USA.
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25
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Diller JR, Thoner TW, Ogden KM. Mammalian orthoreoviruses exhibit rare genotype variability in genome constellations. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 110:105421. [PMID: 36871695 PMCID: PMC10112866 DOI: 10.1016/j.meegid.2023.105421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/21/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Abstract
Mammalian orthoreoviruses (reoviruses) are currently classified based on properties of the attachment protein, σ1. Four reovirus serotypes have been identified, three of which are represented by well-studied prototype human reovirus strains. Reoviruses contain ten segments of double-stranded RNA that encode 12 proteins and can reassort during coinfection. To understand the breadth of reovirus genetic diversity and its potential influence on reassortment, the sequence of the entire genome should be considered. While much is known about the prototype strains, a thorough analysis of all ten reovirus genome segment sequences has not previously been conducted. We analyzed phylogenetic relationships and nucleotide sequence conservation for each of the ten segments of more than 60 complete or nearly complete reovirus genome sequences, including those of the prototype strains. Using these relationships, we defined genotypes for each segment, with minimum nucleotide identities of 77-88% for most genotypes that contain several representative sequences. We applied segment genotypes to determine reovirus genome constellations, and we propose implementation of an updated reovirus genome classification system that incorporates genotype information for each segment. For most sequenced reoviruses, segments other than S1, which encodes σ1, cluster into a small number of genotypes and a limited array of genome constellations that do not differ greatly over time or based on animal host. However, a small number of reoviruses, including prototype strain Jones, have constellations in which segment genotypes differ from those of most other sequenced reoviruses. For these reoviruses, there is little evidence of reassortment with the major genotype. Future basic research studies that focus on the most genetically divergent reoviruses may provide new insights into reovirus biology. Analysis of available partial sequences and additional complete reovirus genome sequencing may also reveal reassortment biases, host preferences, or infection outcomes that are based on reovirus genotype.
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Affiliation(s)
- Julia R Diller
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Timothy W Thoner
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kristen M Ogden
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA.
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26
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Han YJ, Lee KM, Wu GH, Gong YN, Dutta A, Shih SR. Targeting influenza A virus by splicing inhibitor herboxidiene reveals the importance of subtype-specific signatures around splice sites. J Biomed Sci 2023; 30:10. [PMID: 36737756 PMCID: PMC9895974 DOI: 10.1186/s12929-023-00897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 01/05/2023] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The association between M segment splicing and pathogenicity remains ambiguous in human influenza A viruses. In this study, we aimed to investigate M splicing in various human influenza A viruses and characterize its physiological roles by applying the splicing inhibitor, herboxidiene. METHODS We examined the M splicing of human H1N1 and H3N2 viruses by comparing three H1N1 and H3N2 strains, respectively, through reverse transcriptase-polymerase chain reaction (RT-PCR) analyses. We randomly selected M sequences of human H1N1, H2N2, and H3N2 viruses isolated from 1933 to 2020 and examined their phylogenetic relationships. Next, we determined the effects of single nucleotide variations on M splicing by generating mutant viruses harboring the 55C/T variant through reverse genetics. To confirm the importance of M2 splicing in the replication of H1N1 and H3N2, we treated infected cells with splicing inhibitor herboxidiene and analyzed the viral growth using plaque assay. To explore the physiological role of the various levels of M2 protein in pathogenicity, we challenged C57BL/6 mice with the H1N1 WSN wild-type strain, mutant H1N1 (55T), and chimeric viruses including H1N1 + H3wt and H1N1 + H3mut. One-tailed paired t-test was used for virus titer calculation and multiple comparisons between groups were performed using two-way analysis of variance. RESULTS M sequence splice site analysis revealed an evolutionarily conserved single nucleotide variant C55T in H3N2, which impaired M2 expression and was accompanied by collinear M1 and mRNA3 production. Aberrant M2 splicing resulted from splice-site selection rather than a general defect in the splicing process. The C55T substitution significantly reduced both M2 mRNA and protein levels regardless of the virus subtype. Consequently, herboxidiene treatment dramatically decreased both the H1N1 and H3N2 virus titers. However, a lower M2 expression only attenuated H1N1 virus replication and in vivo pathogenicity. This attenuated phenotype was restored by M replacement of H3N2 M in a chimeric H1N1 virus, despite low M2 levels. CONCLUSIONS The discrepancy in M2-dependence emphasizes the importance of M2 in human influenza A virus pathogenicity, which leads to subtype-specific evolution. Our findings provide insights into virus adaptation processes in humans and highlights splicing regulation as a potential antiviral target.
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Affiliation(s)
- Yi-Ju Han
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922International Master Degree Program for Molecular Medicine in Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Guan-Hong Wu
- grid.145695.a0000 0004 1798 0922Graduate Institute of Biomedical Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Nong Gong
- grid.145695.a0000 0004 1798 0922Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan ,grid.454211.70000 0004 1756 999XDepartment of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Avijit Dutta
- grid.454211.70000 0004 1756 999XDivision of Infectious Diseases, Department of Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center of Emerging Virus Infection, Division of Biotechnology, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Department of Laboratory Science, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan. .,Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan. .,Research Center for Chinese Herbal Medicine, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Research Center for Food and Cosmetic Safety, Chang Gung University of Science and Technology, Taoyuan, Taiwan. .,Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
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Sun Y, Zhang T, Zhao X, Qian J, Jiang M, Jia M, Xu Y, Yang W, Feng L. High activity levels of avian influenza upwards 2018–2022: A global epidemiological overview of fowl and human infections. One Health 2023. [DOI: 10.1016/j.onehlt.2023.100511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
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28
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Zhang Y, Shi J, Cui P, Zhang Y, Chen Y, Hou Y, Liu L, Jiang Y, Guan Y, Chen H, Kong H, Deng G. Genetic analysis and biological characterization of H10N3 influenza A viruses isolated in China from 2014 to 2021. J Med Virol 2023; 95:e28476. [PMID: 36609855 DOI: 10.1002/jmv.28476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/22/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023]
Abstract
The H10 subtypes of avian influenza viruses pose a continual threat to the poultry industry and human health. The sporadic spillover of H10 subtypes viruses from poultry to humans is represented by the H10N8 human cases in 2013 and the recent H10N3 human infection in 2021. However, the genesis and characteristics of the recent reassortment H10N3 viruses have not been systemically investigated. In this study, we characterized 20 H10N3 viruses isolated in live poultry markets during routine nationwide surveillance in China from 2014 to 2021. The viruses in the recent reassortant genotype acquired their hemagglutinin (HA) and neuraminidase (NA) genes from the duck H10 viruses and H7N3 viruses, respectively, whereas the internal genes were derived from chicken H9N2 viruses as early as 2019. Receptor-binding analysis indicated that two of the tested H10N3 viruses had a higher affinity for human-type receptors than for avian-type receptors, highlighting the potential risk of avian-to-human transmission. Animal studies showed that only viruses belonging to the recent reassortant genotype were pathogenic in mice; two tested viruses transmitted via direct contact and one virus transmitted by respiratory droplets in guinea pigs, though with limited efficiency. These findings emphasize the need for enhanced surveillance of H10N3 viruses.
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Affiliation(s)
- Yuancheng Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Jianzhong Shi
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Pengfei Cui
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yaping Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yuan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yujie Hou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Liling Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yongping Jiang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Yuntao Guan
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Hualan Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Huihui Kong
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
| | - Guohua Deng
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, CAAS, Harbin, China
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Han J, Zhu X, Gao Z, Xiao Y, Zhang J, Wang P, Fang J, Li Y, Zhu Y, Li Y, Jin N, Lu H, Lin D, Liu W. Antiviral effects of Atractyloside A on the influenza B virus (Victoria strain) infection. Front Microbiol 2023; 13:1067725. [PMID: 36704555 PMCID: PMC9871751 DOI: 10.3389/fmicb.2022.1067725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 12/08/2022] [Indexed: 01/12/2023] Open
Abstract
Influenza viruses pose a serious threat to human health, infecting hundreds of millions of people worldwide each year, resulting in a significant increase in global morbidity and mortality. Influenza activity has declined at the onset of the COVID-19 pandemic, but the genetic diversity of B/Victoria lineage viruses has increased significantly during this period. Therefore, the prevention and treatment of the influenza B Victoria strain virus should continue to attract research attention. In this study, we found that Atractyloside A (AA), one of the effective components in Atractylodes lancea (Thunb.) DC shows potential antiviral properties. This study shows that AA not only possesses anti-influenza B virus infection effects in vivo and in vitro but also can regulate macrophage polarization to the M2 type, which can effectively attenuate the damage caused by influenza B virus infection. Therefore, Atractyloside A may be an effective natural drug against B/Victoria influenza infection.
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Affiliation(s)
- Jicheng Han
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Xiangyu Zhu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Zihan Gao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Yan Xiao
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Jinxin Zhang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Peng Wang
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,College of Animal Science and Technology, Jilin Agricultural University, Changchun, China
| | - Jinbo Fang
- Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Yiquan Li
- Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Yilong Zhu
- Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Yue Li
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China
| | - Ningyi Jin
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Academician Workstation, Changchun University of Chinese Medicine, Changchun, China,*Correspondence: Ningyi Jin ✉
| | - Huijun Lu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Huijun Lu ✉
| | - Dazhuan Lin
- College of Pharmaceuticals and Food, Changchun Medical College, Changchun, China,Dazhuan Lin ✉
| | - Wenshen Liu
- Changchun Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Changchun, China,Wenshen Liu ✉
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30
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Kawasaki J, Tomonaga K, Horie M. Large-scale investigation of zoonotic viruses in the era of high-throughput sequencing. Microbiol Immunol 2023; 67:1-13. [PMID: 36259224 DOI: 10.1111/1348-0421.13033] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/28/2022] [Accepted: 10/16/2022] [Indexed: 01/10/2023]
Abstract
Zoonotic diseases considerably impact public health and socioeconomics. RNA viruses reportedly caused approximately 94% of zoonotic diseases documented from 1990 to 2010, emphasizing the importance of investigating RNA viruses in animals. Furthermore, it has been estimated that hundreds of thousands of animal viruses capable of infecting humans are yet to be discovered, warning against the inadequacy of our understanding of viral diversity. High-throughput sequencing (HTS) has enabled the identification of viral infections with relatively little bias. Viral searches using both symptomatic and asymptomatic animal samples by HTS have revealed hidden viral infections. This review introduces the history of viral searches using HTS, current analytical limitations, and future potentials. We primarily summarize recent research on large-scale investigations on viral infections reusing HTS data from public databases. Furthermore, considering the accumulation of uncultivated viruses, we discuss current studies and challenges for connecting viral sequences to their phenotypes using various approaches: performing data analysis, developing predictive modeling, or implementing high-throughput platforms of virological experiments. We believe that this article provides a future direction in large-scale investigations of potential zoonotic viruses using the HTS technology.
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Affiliation(s)
- Junna Kawasaki
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Faculty of Science and Engineering, Waseda University, Tokyo, Japan
| | - Keizo Tomonaga
- Laboratory of RNA Viruses, Department of Virus Research, Institute for Frontier Life and Medical Sciences, Kyoto University, Kyoto, Japan.,Laboratory of RNA Viruses, Department of Mammalian Regulatory Network, Graduate School of Biostudies, Kyoto University, Kyoto, Japan.,Department of Molecular Virology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masayuki Horie
- Division of Veterinary Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Osaka, Japan.,Osaka International Research Center for Infectious Diseases, Osaka Prefecture University, Osaka, Japan
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31
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Zhu H, Li X, Chen H, Qian P. Genetic characterization and pathogenicity of a Eurasian avian-like H1N1 swine influenza reassortant virus. Virol J 2022; 19:205. [PMID: 36461007 PMCID: PMC9716174 DOI: 10.1186/s12985-022-01936-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/27/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND Swine influenza viruses (SIV), considered the "mixing vessels" of influenza viruses, posed a significant threat to global health systems and are dangerous pathogens. Eurasian avian-like H1N1(EA-H1N1) viruses have become predominant in swine populations in China since 2016. METHODS Lung tissue samples were obtained from pregnant sows with miscarriage and respiratory disease in Heilongjiang province, and pathogens were detected by Next-generation sequencing (NGS) and PCR. The nucleic acid of isolates was extracted to detect SIV by RT-PCR. Then, SIV-positive samples were inoculated into embryonated chicken eggs. After successive generations, the isolates were identified by RT-PCR, IFA, WB and TEM. The genetic evolution and pathogenicity to mice of A/swine/Heilongjiang/GN/2020 were analyzed. RESULTS The major pathogens were influenza virus (31%), Simbu orthobunyavirus (15%) and Jingmen tick virus (8%) by NGS, while the pathogen that can cause miscarriage and respiratory disease was influenza virus. The SIV(A/swine/Heilongjiang/GN/2020) with hemagglutination activity was isolated from lung samples and was successfully identified by RT-PCR, IFA, WB and TEM. Homology and phylogenetic analysis showed that A/swine/Heilongjiang/GN/2020 is most closely related to A/swine/Henan/SN/10/2018 and belonged to EA-H1N1. Pathogenicity in mice showed that the EA-H1N1 could cause lethal or exhibit extrapulmonary virus spread and cause severe damage to respiratory tracts effectively proliferating in lung and trachea. CONCLUSION A/swine/Heilongjiang/GN/2020 (EA-H1N1) virus was isolated from pregnant sows with miscarriage and respiratory disease in Heilongjiang province, China. Clinical signs associated with influenza infection were observed during 14 days with A/swine/Heilongjiang/GN/2020 infected mice. These data suggest that A/swine/Heilongjiang/GN/2020 (EA-H1N1) had high pathogenicity and could be systemic spread in mice.
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Affiliation(s)
- Hechao Zhu
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
| | - Xiangmin Li
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
| | - Huanchun Chen
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
| | - Ping Qian
- grid.35155.370000 0004 1790 4137State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China ,grid.35155.370000 0004 1790 4137Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, 430070 Hubei China
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32
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Kolosova NP, Ilyicheva TN, Unguryan VV, Danilenko AV, Svyatchenko SV, Onhonova GS, Goncharova NI, Kosenko MN, Gudymo AS, Marchenko VY, Shvalov AN, Susloparov IM, Tregubchak TV, Gavrilova EV, Maksyutov RA, Ryzhikov AB. Re-Emergence of Circulation of Seasonal Influenza during COVID-19 Pandemic in Russia and Receptor Specificity of New and Dominant Clade 3C.2a1b.2a.2 A(H3N2) Viruses in 2021-2022. Pathogens 2022; 11:1388. [PMID: 36422639 PMCID: PMC9698969 DOI: 10.3390/pathogens11111388] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/18/2022] [Indexed: 11/29/2023] Open
Abstract
The circulation of seasonal influenza in 2020-2021 around the world was drastically reduced after the start of the COVID-19 pandemic and the implementation of mitigation strategies. The influenza virus circulation reemerged in 2021-2022 with the global spread of the new genetic clade 3C.2a1b.2a.2 of A(H3N2) viruses. The purpose of this study was to characterize influenza viruses in the 2021-2022 season in Russia and to analyze the receptor specificity properties of the 3C.2a1b.2a.2 A(H3N2) viruses. Clinical influenza samples were collected at the local Sanitary-and-Epidemiological Centers of Rospotrebnadzor. Whole genome sequencing was performed using NGS. The receptor specificity of hemagglutinin was evaluated using molecular modeling and bio-layer interferometry. Clinical samples from 854 cases of influenza A and B were studied; A(H3N2) viruses were in the majority of the samples. All genetically studied A(H3N2) viruses belonged to the new genetic clade 3C.2a1b.2a.2. Molecular modeling analysis suggested a higher affinity of hemagglutinin of 3C.2a1b.2a.2. A(H3N2) viruses to the α2,6 human receptor. In vitro analysis using a trisaccharide 6'-Sialyl-N-acetyllactosamine receptor analog did not resolve the differences in the receptor specificity of 3C.2a1b.2a.2 clade viruses from viruses belonging to the 3C.2a1b.2a.1 clade. Further investigation of the A(H3N2) viruses is required for the evaluation of their possible adaptive advantages. Constant monitoring and characterization of influenza are critical for epidemiological analysis.
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Affiliation(s)
- Natalia P. Kolosova
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Tatiana N. Ilyicheva
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Vasily V. Unguryan
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
- Department of Physics, Novosibirsk State University, Novosibirsk 630090, Russia
| | - Alexey V. Danilenko
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Svetlana V. Svyatchenko
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Galina S. Onhonova
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Natalia I. Goncharova
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Maksim N. Kosenko
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Andrey S. Gudymo
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Vasiliy Y. Marchenko
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Alexander N. Shvalov
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Ivan M. Susloparov
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Tatiana V. Tregubchak
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Elena V. Gavrilova
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Rinat A. Maksyutov
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
| | - Alexander B. Ryzhikov
- State Research Centre of Virology and Biotechnology “Vector”, Rospotrebnadzor, Koltsovo, Novosibirsk 630559, Russia
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A new nanobody-enzyme fusion protein-linked immunoassay for detecting antibodies against influenza A virus in different species. J Biol Chem 2022; 298:102709. [PMID: 36402446 PMCID: PMC9763686 DOI: 10.1016/j.jbc.2022.102709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/09/2022] [Accepted: 11/10/2022] [Indexed: 11/18/2022] Open
Abstract
Circulation of influenza A virus (IAV), especially within poultry and pigs, continues to threaten public health. A simple and universal detecting method is important for monitoring IAV infection in different species. Recently, nanobodies, which show advantages of easy gene editing and low cost of production, are a promising novel diagnostic tool for the monitoring and control of global IAVs. In the present study, five nanobodies against the nucleoprotein of H9N2 IAV were screened from the immunized Bactrian camel by phage display and modified with horseradish peroxidase (HRP) tags. Out of which, we determined that H9N2-NP-Nb5-HRP can crossreact with different subtypes of IAVs, and this reaction is also blocked by positive sera for antibodies against different IAV subtypes. Epitope mapping showed that the nanobody-HRP fusion recognized a conserved conformational epitope in all subtypes of IAVs. Subsequently, we developed a nanobody-based competitive ELISA (cELISA) for detecting anti-IAV antibodies in different species. The optimized amount of coating antigen and dilutions of the fusion and testing sera were 100 ng/well, 1:4000, and 1:10, respectively. The time for operating the cELISA was approximately 35 min. The cELISA showed high sensitivity, specificity, reproducibility, and stability. In addition, we found that the cELISA and hemagglutination inhibition test showed a consistency of 100% and 87.91% for clinical and challenged chicken sera, respectively. Furthermore, the agreement rates were 90.4% and 85.7% between the cELISA and commercial IEDXX ELISA kit. Collectively, our developed nanobody-HRP fusion-based cELISA is an ideal method for monitoring IAV infection in different species.
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Zhu H, Li X, Ren X, Chen H, Qian P. Improving cross-protection against influenza virus in mice using a nanoparticle vaccine of mini-HA. Vaccine 2022; 40:6352-6361. [PMID: 36175214 DOI: 10.1016/j.vaccine.2022.09.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 09/02/2022] [Accepted: 09/19/2022] [Indexed: 01/27/2023]
Abstract
This study aimed to investigate the protective effect of mini-hemagglutinin (mini-HA) proteins expressed on lumazine synthase (LS) nanoparticles against influenza. Soluble mini-HA proteins were assembled with LS proteins via SpyTag/SpyCatcher in vitro. The size of mini-HA-LS nanoparticles was characterized by transmission electron microscopy (TEM) and dynamic light scattering (DLS), and the effect of mini-HA-LS nano-vaccines was explored in mice. The results indicate that the diameter of mini-HA-LS nanoparticles was approximately 60-80 nm. The nanoparticles could induce stronger humoral and cellular immune responses and produce cross-clade protection against influenza in mice.
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Affiliation(s)
- Hechao Zhu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Xiangmin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Xujiao Ren
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Laboratory of Animal Virology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, Hubei, China; Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, Hubei 430070, China.
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Song H, Liu X, Gao X, Li J, Shang Y, Gao W, Li Y, Zhang Z. Transcriptome analysis of pre-immune state induced by interferon gamma inhibiting the replication of H 9N 2 avian influenza viruses in chicken embryo fibroblasts. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 103:105332. [PMID: 35811034 DOI: 10.1016/j.meegid.2022.105332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/24/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
Interferon (IFN), a critical antiviral cytokine produced by pathogens-induced cells, plays an important role in host innate immune system. In this study, to investigate the inhibition effect of IFN on avian influenza virus (AIV), Chicken Embryo Fibroblasts (CEFs) was infected by H9N2 AIV. The pre-immune state and transcriptome analysis have been observed and performed. The result showed chicken interferon gamma (chIFN-γ) have the most inhibitory effect on H9N2 virus among three types of chicken interferons (chIFNs). Inhibition of chIFN-γ on H9N2 virus was verified by indirect immunofluorescence, RT-qPCR and western blot. The possible signaling pathways induced by chIFN-γ with or without virus were analyzed by transcriptome. The transcriptome data were compared among H9N2-infected, chIFN-γ-treated, chIFN-γ + H9N2-treated, and Control groups. In summary, RNA-sequencing (RNA-seq) data suggested that H9N2 virus infection resulted in corresponding response of certain defensive, inflammatory and metabolism pathways to the virus replication in CEFs. Furthermore, while CEFs were treated with chIFN-γ, many immune-related signaling pathways in cells are affected and altered. Antiviral genes involved in these immune pathways such as interferon regulatory factors, chemokines, interferon-stimulated genes (ISGs) and transcription factors were significantly up-regulated, and showed significant antiviral responses. Compared with virus infected CEFs alone, pretreatment with IFN induced the expression of antiviral genes and activated related antiviral pathways, inhibited the viral replication as result. Our study provided functional annotations for antiviral genes and the basis for studying the mechanism of chIFN-γ mediated response against H9N2 AIV.
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Affiliation(s)
- Haozhi Song
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xingjian Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xintao Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jialei Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuting Shang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weisong Gao
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yinü Li
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Zhifang Zhang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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36
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Varghese PM, Kishore U, Rajkumari R. Innate and adaptive immune responses against Influenza A Virus: Immune evasion and vaccination strategies. Immunobiology 2022; 227:152279. [DOI: 10.1016/j.imbio.2022.152279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/31/2022] [Accepted: 09/07/2022] [Indexed: 11/25/2022]
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Wille M, Tolf C, Latorre-Margalef N, Fouchier RAM, Halpin RA, Wentworth DE, Ragwani J, Pybus OG, Olsen B, Waldenström J. Evolutionary features of a prolific subtype of avian influenza A virus in European waterfowl. Virus Evol 2022; 8:veac074. [PMID: 36128050 PMCID: PMC9477075 DOI: 10.1093/ve/veac074] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 06/12/2022] [Accepted: 08/25/2022] [Indexed: 11/26/2022] Open
Abstract
Avian influenza A virus (AIV) is ubiquitous in waterfowl and is detected annually at high prevalence in waterfowl during the Northern Hemisphere autumn. Some AIV subtypes are globally common in waterfowl, such as H3N8, H4N6, and H6N2, and are detected in the same populations at a high frequency, annually. In order to investigate genetic features associated to the long-term maintenance of common subtypes in migratory ducks, we sequenced 248 H4 viruses isolated across 8 years (2002-9) from mallards (Anas platyrhynchos) sampled in southeast Sweden. Phylogenetic analyses showed that both H4 and N6 sequences fell into three distinct lineages, structured by year of isolation. Specifically, across the 8 years of the study, we observed lineage replacement, whereby a different HA lineage circulated in the population each year. Analysis of deduced amino acid sequences of the HA lineages illustrated key differences in regions of the globular head of hemagglutinin that overlap with established antigenic sites in homologous hemagglutinin H3, suggesting the possibility of antigenic differences among these HA lineages. Beyond HA, lineage replacement was common to all segments, such that novel genome constellations were detected across years. A dominant genome constellation would rapidly amplify in the duck population, followed by unlinking of gene segments as a result of reassortment within 2-3 weeks following introduction. These data help reveal the evolutionary dynamics exhibited by AIV on both annual and decadal scales in an important reservoir host.
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Affiliation(s)
- Michelle Wille
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Conny Tolf
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Neus Latorre-Margalef
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
| | - Ron A M Fouchier
- Department of Virology, Erasmus Medical Centre, Rotterdam, The Netherlands
| | | | | | - Jayna Ragwani
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3SY, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London AL9 7TA, UK
| | - Björn Olsen
- Section of Infectious Diseases, Department of Medical Sciences, Uppsala University, Uppsala SE751 85, Sweden
| | - Jonas Waldenström
- Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Universitetsplatsen 1, Kalmar SE-39231, Sweden
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Yang L, Van Beek M, Wang Z, Muecksch F, Canis M, Hatziioannou T, Bieniasz PD, Nussenzweig MC, Chakraborty AK. Antigen presentation dynamics shape the response to emergent variants like SARS-CoV-2 Omicron strain after multiple vaccinations with wild type strain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.24.505127. [PMID: 36052368 PMCID: PMC9435403 DOI: 10.1101/2022.08.24.505127] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Omicron variant of SARS-CoV-2 evades neutralization by most serum antibodies elicited by two doses of mRNA vaccines, but a third dose of the same vaccine increases anti-Omicron neutralizing antibodies. By combining computational modeling with data from vaccinated humans we reveal mechanisms underlying this observation. After the first dose, limited antigen availability in germinal centers results in a response dominated by B cells with high germline affinities for immunodominant epitopes that are significantly mutated in an Omicron-like variant. After the second dose, expansion of these memory cells and differentiation into plasma cells shape antibody responses that are thus ineffective for such variants. However, in secondary germinal centers, pre-existing higher affinity antibodies mediate enhanced antigen presentation and they can also partially mask dominant epitopes. These effects generate memory B cells that target subdominant epitopes that are less mutated in Omicron. The third dose expands these cells and boosts anti-variant neutralizing antibodies.
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Affiliation(s)
- Leerang Yang
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Matthew Van Beek
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Zijun Wang
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
| | - Frauke Muecksch
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | - Marie Canis
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
| | | | - Paul D Bieniasz
- Laboratory of Retrovirology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Michel C Nussenzweig
- Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute
| | - Arup K Chakraborty
- Departments of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Physics, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139
- Institute for Medical Engineering & Science, Massachusetts Institute of Technology; Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology, and Harvard, Cambridge, MA 02139
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Co-existence and co-infection of influenza A viruses and coronaviruses: Public health challenges. Innovation (N Y) 2022; 3:100306. [PMID: 35992368 PMCID: PMC9384331 DOI: 10.1016/j.xinn.2022.100306] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/14/2022] [Indexed: 02/08/2023] Open
Abstract
Since the 20th century, humans have lived through five pandemics caused by influenza A viruses (IAVs) (H1N1/1918, H2N2/1957, H3N2/1968, and H1N1/2009) and the coronavirus (CoV) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IAVs and CoVs both have broad host ranges and share multiple hosts. Virus co-circulation and even co-infections facilitate genetic reassortment among IAVs and recombination among CoVs, further altering virus evolution dynamics and generating novel variants with increased cross-species transmission risk. Moreover, SARS-CoV-2 may maintain long-term circulation in humans as seasonal IAVs. Co-existence and co-infection of both viruses in humans could alter disease transmission patterns and aggravate disease burden. Herein, we demonstrate how virus-host ecology correlates with the co-existence and co-infection of IAVs and/or CoVs, further affecting virus evolution and disease dynamics and burden, calling for active virus surveillance and countermeasures for future public health challenges.
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Zupin L, dos Santos-Silva CA, Al Mughrbi ARH, Vilela LMB, Benko-Iseppon AM, Crovella S. Bioactive Antimicrobial Peptides: A New Weapon to Counteract Zoonosis. Microorganisms 2022; 10:microorganisms10081591. [PMID: 36014009 PMCID: PMC9414035 DOI: 10.3390/microorganisms10081591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Zoonoses have recently become the center of attention of the general population and scientific community. Notably, more than 30 new human pathogens have been identified in the last 30 years, 75% of which can be classified as zoonosis. The complete eradication of such types of infections is far out of reach, considering the limited understanding of animal determinants in zoonoses and their causes of emergence. Therefore, efforts must be doubled in examining the spread, persistence, and pathogenicity of zoonosis and studying possible clinical interventions and antimicrobial drug development. The search for antimicrobial bioactive compounds has assumed great emphasis, considering the emergence of multi-drug-resistant microorganisms. Among the biomolecules of emerging scientific interest are antimicrobial peptides (AMPs), potent biomolecules that can potentially act as important weapons against infectious diseases. Moreover, synthetic AMPs are easily tailored (bioinformatically) to target specific features of the pathogens to hijack, inducing no or very low resistance. Although very promising, previous studies on SAMPs’ efficacy are still at their early stages. Indeed, further studies and better characterization on their mechanism of action with in vitro and in vivo assays are needed so as to proceed to their clinical application on human beings.
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Affiliation(s)
- Luisa Zupin
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy
- Correspondence: (L.Z.); (S.C.)
| | | | | | - Livia Maria Batista Vilela
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Ana Maria Benko-Iseppon
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
- Correspondence: (L.Z.); (S.C.)
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Nogales A, Steel J, Liu WC, Lowen AC, Rodriguez L, Chiem K, Cox A, García-Sastre A, Albrecht RA, Dewhurst S, Martínez-Sobrido L. Mutation L319Q in the PB1 Polymerase Subunit Improves Attenuation of a Candidate Live-Attenuated Influenza A Virus Vaccine. Microbiol Spectr 2022; 10:e0007822. [PMID: 35583364 PMCID: PMC9241597 DOI: 10.1128/spectrum.00078-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 04/25/2022] [Indexed: 01/11/2023] Open
Abstract
Influenza A viruses (IAV) remain emerging threats to human public health. Live-attenuated influenza vaccines (LAIV) are one of the most effective prophylactic options to prevent disease caused by influenza infections. However, licensed LAIV remain restricted for use in 2- to 49-year-old healthy and nonpregnant people. Therefore, development of LAIV with increased safety, immunogenicity, and protective efficacy is highly desired. The U.S.-licensed LAIV is based on the master donor virus (MDV) A/Ann Arbor/6/60 H2N2 backbone, which was generated by adaptation of the virus to growth at low temperatures. Introducing the genetic signature of the U.S. MDV into the backbone of other IAV strains resulted in varying levels of attenuation. While the U.S. MDV mutations conferred an attenuated phenotype to other IAV strains, the same amino acid changes did not significantly attenuate the pandemic A/California/04/09 H1N1 (pH1N1) strain. To attenuate pH1N1, we replaced the conserved leucine at position 319 with glutamine (L319Q) in PB1 and analyzed the in vitro and in vivo properties of pH1N1 viruses containing either PB1 L319Q alone or in combination with the U.S. MDV mutations using two animal models of influenza infection and transmission, ferrets and guinea pigs. Our results demonstrated that L319Q substitution in the pH1N1 PB1 alone or in combination with the mutations of the U.S. MDV resulted in reduced pathogenicity (ferrets) and transmission (guinea pigs), and an enhanced temperature sensitive phenotype. These results demonstrate the feasibility of generating an attenuated MDV based on the backbone of a contemporary pH1N1 IAV strain. IMPORTANCE Vaccination represents the most effective strategy to reduce the impact of seasonal IAV infections. Although LAIV are superior in inducing protection and sterilizing immunity, they are not recommended for many individuals who are at high risk for severe disease. Thus, development of safer and more effective LAIV are needed. A concern with the current MDV used to generate the U.S.-licensed LAIV is that it is based on a virus isolated in 1960. Moreover, mutations that confer the temperature-sensitive, cold-adapted, and attenuated phenotype of the U.S. MDV resulted in low level of attenuation in the contemporary pandemic A/California/04/09 H1N1 (pH1N1). Here, we show that introduction of PB1 L319Q substitution, alone or in combination with the U.S. MDV mutations, resulted in pH1N1 attenuation. These findings support the development of a novel LAIV MDV based on a contemporary pH1N1 strain as a medical countermeasure against currently circulating H1N1 IAV.
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Affiliation(s)
- Aitor Nogales
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Animal Health Research Centre (CISA), Centro Nacional Instituto de Investigación y Tecnología Agraria y Alimentaria (INIA, CSIC), Madrid, Spain
| | - John Steel
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Wen-Chun Liu
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Biomedical Translation Research Center, Academia Sinica, Taipei, Taiwan
| | - Anice C. Lowen
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Laura Rodriguez
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Agencia Española de Medicamentos y Productos Sanitarios, Madrid, Spain
| | - Kevin Chiem
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Texas Biomedical Research Institute, San Antonio, Texas, USA
| | - Andrew Cox
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Adolfo García-Sastre
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Medicine, Division of Infectious Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Randy A. Albrecht
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Global Health and Emerging Pathogens Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Stephen Dewhurst
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
- Texas Biomedical Research Institute, San Antonio, Texas, USA
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42
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Current Opinion in LAIV: A Matter of Parent Virus Choice. Int J Mol Sci 2022; 23:ijms23126815. [PMID: 35743258 PMCID: PMC9224562 DOI: 10.3390/ijms23126815] [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: 04/16/2022] [Revised: 06/16/2022] [Accepted: 06/17/2022] [Indexed: 01/26/2023] Open
Abstract
Influenza is still a frequent seasonal infection of the upper respiratory tract, which may have deadly consequences, especially for the elderly. This is in spite of the availability of vaccines suggested for persons above 65 years of age. Two types of conventional influenza vaccines are currently licensed for use-live attenuated and inactivated vaccines. Depending on local regulatory requirements, live attenuated vaccines are produced by the reverse genetics technique or by classical reassortment in embryonated chicken eggs. Sometimes, the efficiency of classical reassortment is complicated by certain properties of the wild-type parent virus. Cases of low efficacy of vaccines have been noted, which, among other reasons, may be associated with suboptimal properties of the wild-type parent virus that are not considered when recommendations for influenza vaccine composition are made. Unfortunately, knowledge surrounding the roles of properties of the circulating influenza virus and its impact on the efficacy of the reassortment process, vaccination efficiency, the infectivity of the vaccine candidates, etc., is now scattered in different publications. This review summarizes the main features of the influenza virus that may dramatically affect different aspects of the preparation of egg-derived live attenuated vaccine candidates and their effectiveness. The author expresses her personal view, which may not coincide with the opinion of other experts in the field of influenza vaccines.
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43
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He D, Wang X, Wu H, Wang X, Yan Y, Li Y, Zhan T, Hao X, Hu J, Hu S, Liu X, Ding C, Su S, Gu M, Liu X. Genome-Wide Reassortment Analysis of Influenza A H7N9 Viruses Circulating in China during 2013-2019. Viruses 2022; 14:v14061256. [PMID: 35746727 PMCID: PMC9230085 DOI: 10.3390/v14061256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/29/2022] [Accepted: 06/06/2022] [Indexed: 11/16/2022] Open
Abstract
Reassortment with the H9N2 virus gave rise to the zoonotic H7N9 avian influenza virus (AIV), which caused more than five outbreak waves in humans, with high mortality. The frequent exchange of genomic segments between H7N9 and H9N2 has been well-documented. However, the reassortment patterns have not been described and are not yet fully understood. Here, we used phylogenetic analyses to investigate the patterns of intersubtype and intrasubtype/intralineage reassortment across the eight viral segments. The H7N9 virus and its progeny frequently exchanged internal genes with the H9N2 virus but rarely with the other AIV subtypes. Before beginning the intrasubtype/intralineage reassortment analyses, five Yangtze River Delta (YRD A-E) and two Pearl River Delta (PRD A-B) clusters were divided according to the HA gene phylogeny. The seven reset segment genes were also nomenclatured consistently. As revealed by the tanglegram results, high intralineage reassortment rates were determined in waves 2–3 and 5. Additionally, the clusters of PB2 c05 and M c02 were the most dominant in wave 5, which could have contributed to the onset of the largest H7N9 outbreak in 2016–2017. Meanwhile, a portion of the YRD-C cluster (HP H7N9) inherited their PB2, PA, and M segments from the co-circulating YRD-E (LP H7N9) cluster during wave 5. Untanglegram results revealed that the reassortment rate between HA and NA was lower than HA with any of the other six segments. A multidimensional scaling plot revealed a robust genetic linkage between the PB2 and PA genes, indicating that they may share a co-evolutionary history. Furthermore, we observed relatively more robust positive selection pressure on HA, NA, M2, and NS1 proteins. Our findings demonstrate that frequent reassortment, particular reassorted patterns, and adaptive mutations shaped the H7N9 viral genetic diversity and evolution. Increased surveillance is required immediately to better understand the current state of the HP H7N9 AIV.
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Affiliation(s)
- Dongchang He
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiyue Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Huiguang Wu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiaoquan Wang
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Yayao Yan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Yang Li
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Tiansong Zhan
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Xiaoli Hao
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
| | - Jiao Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Shunlin Hu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Xiaowen Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
| | - Chan Ding
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai 200241, China
| | - Shuo Su
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
| | - Min Gu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (M.G.); (X.L.)
| | - Xiufan Liu
- Animal Infectious Disease Laboratory, College of Veterinary Medicine, Yangzhou University, Yangzhou 225009, China; (D.H.); (X.W.); (H.W.); (X.W.); (Y.Y.); (Y.L.); (T.Z.); (X.H.); (J.H.); (S.H.); (X.L.)
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonosis, Yangzhou University, Yangzhou 225009, China;
- Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou 225009, China
- Correspondence: (M.G.); (X.L.)
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Krischuns T, Isel C, Drncova P, Lukarska M, Pflug A, Paisant S, Navratil V, Cusack S, Naffakh N. Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD. PLoS Pathog 2022; 18:e1010328. [PMID: 35605026 PMCID: PMC9242477 DOI: 10.1371/journal.ppat.1010328] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/29/2022] [Accepted: 04/09/2022] [Indexed: 01/05/2023] Open
Abstract
During annual influenza epidemics, influenza B viruses (IBVs) co-circulate with influenza A viruses (IAVs), can become predominant and cause severe morbidity and mortality. Phylogenetic analyses suggest that IAVs (primarily avian viruses) and IBVs (primarily human viruses) have diverged over long time scales. Identifying their common and distinctive features is an effective approach to increase knowledge about the molecular details of influenza infection. The virus-encoded RNA-dependent RNA polymerases (FluPolB and FluPolA) are PB1-PB2-PA heterotrimers that perform transcription and replication of the viral genome in the nucleus of infected cells. Initiation of viral mRNA synthesis requires a direct association of FluPol with the host RNA polymerase II (RNAP II), in particular the repetitive C-terminal domain (CTD) of the major RNAP II subunit, to enable "cap-snatching" whereby 5'-capped oligomers derived from nascent RNAP II transcripts are pirated to prime viral transcription. Here, we present the first high-resolution co-crystal structure of FluPolB bound to a CTD mimicking peptide at a binding site crossing from PA to PB2. By performing structure-based mutagenesis of FluPolB and FluPolA followed by a systematic investigation of FluPol-CTD binding, FluPol activity and viral phenotype, we demonstrate that IBVs and IAVs have evolved distinct binding interfaces to recruit the RNAP II CTD, despite the CTD sequence being highly conserved across host species. We find that the PB2 627 subdomain, a major determinant of FluPol-host cell interactions and IAV host-range, is involved in CTD-binding for IBVs but not for IAVs, and we show that FluPolB and FluPolA bind to the host RNAP II independently of the CTD. Altogether, our results suggest that the CTD-binding modes of IAV and IBV may represent avian- and human-optimized binding modes, respectively, and that their divergent evolution was shaped by the broader interaction network between the FluPol and the host transcriptional machinery.
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Affiliation(s)
- Tim Krischuns
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Catherine Isel
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Petra Drncova
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Maria Lukarska
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Alexander Pflug
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
| | - Sylvain Paisant
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
| | - Vincent Navratil
- PRABI, Rhône Alpes Bioinformatics Center, UCBL, Lyon1, Université de Lyon, Lyon, France
| | - Stephen Cusack
- European Molecular Biology Laboratory, 71 Avenue des Martyrs, Grenoble, France
- * E-mail: (SC); (NN)
| | - Nadia Naffakh
- Institut Pasteur, Université Paris Cité, CNRS UMR3569, Unité Biologie des ARN et Virus Influenza, Paris, France
- * E-mail: (SC); (NN)
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Deviatkin AA, Simonov RA, Trutneva KA, Maznina AA, Khavina EM, Volchkov PY. Universal Flu mRNA Vaccine: Promises, Prospects, and Problems. Vaccines (Basel) 2022; 10:vaccines10050709. [PMID: 35632465 PMCID: PMC9145388 DOI: 10.3390/vaccines10050709] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 04/26/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023] Open
Abstract
The seasonal flu vaccine is, essentially, the only known way to prevent influenza epidemics. However, this approach has limited efficacy due to the high diversity of influenza viruses. Several techniques could potentially overcome this obstacle. A recent first-in-human study of a chimeric hemagglutinin-based universal influenza virus vaccine demonstrated promising results. The coronavirus pandemic triggered the development of fundamentally new vaccine platforms that have demonstrated their effectiveness in humans. Currently, there are around a dozen messenger RNA and self-amplifying RNA flu vaccines in clinical or preclinical trials. However, the applicability of novel approaches for a universal influenza vaccine creation remains unclear. The current review aims to cover the current state of this problem and to suggest future directions for RNA-based flu vaccine development.
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Affiliation(s)
- Andrei A. Deviatkin
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Ruslan A. Simonov
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Kseniya A. Trutneva
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Anna A. Maznina
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Elena M. Khavina
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
| | - Pavel Y. Volchkov
- The National Medical Research Center for Endocrinology, 117036 Moscow, Russia; (A.A.D.); (K.A.T.)
- Genome Engineering Lab, Life Sciences Research Center, Moscow Institute of Physics and Technology (National Research University), 141700 Dolgoprudniy, Russia; (R.A.S.); (A.A.M.); (E.M.K.)
- Correspondence:
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Nogales A, Chiem K, Breen M, DeDiego ML, Parrish CR, Martínez-Sobrido L. Generation and Characterization of Single-Cycle Infectious Canine Influenza A Virus (sciCIV) and Its Use as Vaccine Platform. Methods Mol Biol 2022; 2465:227-255. [PMID: 35118625 DOI: 10.1007/978-1-0716-2168-4_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Influenza A viruses (IAVs) infect a broad range of hosts, including multiple avian and mammalian species. The frequent emergence of novel IAV strains in different hosts, including in humans, results in the need for vigilance and ongoing development of new approaches to fighting or prevent those infections. Canine influenza is a contagious respiratory disease in dogs caused by two subtypes of IAV, the equine-origin H3N8 canine influenza virus (CIV), and the avian-origin H3N2 CIV. A novel approach to influenza vaccination involves single-cycle infectious influenza A viruses (sciIAVs), which are defective for an essential viral gene. They are propagated in complementing cell lines which provide the missing gene in trans. As sciIAV cannot complete their replication cycle in regular cells they are limited to a single round of viral replication. Because of their safety profile and ability to express foreign antigens inside infected cells, sciIAVs have served both as live-attenuated vaccines and as vaccine vectors for the expression of heterologous antigens. Here, we describe experimental procedures for the generation of a single-cycle infectious CIV (sciCIV), where the viral hemagglutinin (HA) gene was exchanged for the gene for green fluorescent protein (GFP). Complementation of the viral HA protein is provided in trans by stable HA-expressing cell lines. Methods for the in vitro characterization of HA deficient but GFP-expressing sciCIV (sciCIV ΔHA/GFP) are described, as well as its use as a potential vaccine.
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Affiliation(s)
- Aitor Nogales
- Centro de Investigación en Sanidad Animal (CISA), INIA-CSIC, Madrid, Spain.
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.
| | - Kevin Chiem
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
- Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Michael Breen
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
- Boston University School of Medicine, Boston, MA, USA
| | - Marta L DeDiego
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA
- Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Colin R Parrish
- Department of Microbiology and Immunology, College of Veterinary Medicine, Baker Institute for Animal Health, Cornell University, Ithaca, NY, USA
| | - Luis Martínez-Sobrido
- Department of Microbiology and Immunology, University of Rochester Medical Center, Rochester, NY, USA.
- Texas Biomedical Research Institute, San Antonio, TX, USA.
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Buchy P, Buisson Y, Cintra O, Dwyer DE, Nissen M, Ortiz de Lejarazu R, Petersen E. COVID-19 pandemic: lessons learned from more than a century of pandemics and current vaccine development for pandemic control. Int J Infect Dis 2021; 112:300-317. [PMID: 34563707 PMCID: PMC8459551 DOI: 10.1016/j.ijid.2021.09.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 09/17/2021] [Accepted: 09/19/2021] [Indexed: 01/04/2023] Open
Abstract
Pandemic dynamics and health care responses are markedly different during the COVID-19 pandemic than in earlier outbreaks. Compared with established infectious disease such as influenza, we currently know relatively little about the origin, reservoir, cross-species transmission and evolution of SARS-CoV-2. Health care services, drug availability, laboratory testing, research capacity and global governance are more advanced than during 20th century pandemics, although COVID-19 has highlighted significant gaps. The risk of zoonotic transmission and an associated new pandemic is rising substantially. COVID-19 vaccine development has been done at unprecedented speed, with the usual sequential steps done in parallel. The pandemic has illustrated the feasibility of this approach and the benefits of a globally coordinated response and infrastructure. Some of the COVID-19 vaccines recently developed or currently in development might offer flexibility or sufficiently broad protection to swiftly respond to antigenic drift or emergence of new coronaviruses. Yet many challenges remain, including the large-scale production of sufficient quantity of vaccines, delivery of vaccines to all countries and ensuring vaccination of relevant age groups. This wide vaccine technology approach will be best employed in tandem with active surveillance for emerging variants or new pathogens using antigen mapping, metagenomics and next generation sequencing.
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Affiliation(s)
- Philippe Buchy
- GSK, Singapore, Singapore,Corresponding author. Philippe Buchy
| | | | | | - Dominic E. Dwyer
- New South Wales Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead Hospital, New South Wales, Australia
| | - Michael Nissen
- Consultant in Infectious Diseases, University of Queensland, Brisbane, Australia
| | - Raul Ortiz de Lejarazu
- Scientific Advisor & Emeritus director at Valladolid NIC (National Influenza Centre) Spain, School of Medicine, Avd Ramón y Cajal s/n 47005 Valladolid, Spain
| | - Eskild Petersen
- European Society for Clinical Microbiology and Infectious Diseases, Basel, Switzerland,Department of Molecular Medicine, The University of Pavia, Pavia, Italy,Department of Clinical, Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
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Nogales A, Villamayor L, Utrilla-Trigo S, Ortego J, Martinez-Sobrido L, DeDiego ML. Natural Selection of H5N1 Avian Influenza A Viruses with Increased PA-X and NS1 Shutoff Activity. Viruses 2021; 13:v13091760. [PMID: 34578340 PMCID: PMC8472985 DOI: 10.3390/v13091760] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/01/2022] Open
Abstract
Influenza A viruses (IAV) can infect a broad range of mammalian and avian species. However, the host innate immune system provides defenses that restrict IAV replication and infection. Likewise, IAV have evolved to develop efficient mechanisms to counteract host antiviral responses to efficiently replicate in their hosts. The IAV PA-X and NS1 non-structural proteins are key virulence factors that modulate innate immune responses and virus pathogenicity during infection. To study the determinants of IAV pathogenicity and their functional co-evolution, we evaluated amino acid differences in the PA-X and NS1 proteins of early (1996–1997) and more recent (since 2016) H5N1 IAV. H5N1 IAV have zoonotic and pandemic potential and represent an important challenge both in poultry farming and human health. The results indicate that amino acid changes occurred over time, affecting the ability of these two non-structural H5N1 IAV proteins to inhibit gene expression and affecting virus pathogenicity. These results highlight the importance to monitor the evolution of these two virulence factors of IAV, which could result in enhanced viral replication and virulence.
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Affiliation(s)
- Aitor Nogales
- Center for Animal Health Research, CISA-INIA-CSIC, Valdeolmos, 28130 Madrid, Spain; (S.U.-T.); (J.O.)
- Correspondence: (A.N.); (M.L.D.)
| | - Laura Villamayor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain;
| | - Sergio Utrilla-Trigo
- Center for Animal Health Research, CISA-INIA-CSIC, Valdeolmos, 28130 Madrid, Spain; (S.U.-T.); (J.O.)
| | - Javier Ortego
- Center for Animal Health Research, CISA-INIA-CSIC, Valdeolmos, 28130 Madrid, Spain; (S.U.-T.); (J.O.)
| | - Luis Martinez-Sobrido
- Department of Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX 78227, USA;
| | - Marta L. DeDiego
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología (CNB-CSIC), Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain;
- Correspondence: (A.N.); (M.L.D.)
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Croze M, Kim Y. Inference of population genetic parameters from an irregular time series of seasonal influenza virus sequences. Genetics 2021; 217:6066165. [PMID: 33724414 DOI: 10.1093/genetics/iyaa039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 12/17/2020] [Indexed: 11/12/2022] Open
Abstract
Basic summary statistics that quantify the population genetic structure of influenza virus are important for understanding and inferring the evolutionary and epidemiological processes. However, the sampling dates of global virus sequences in the last several decades are scattered nonuniformly throughout the calendar. Such temporal structure of samples and the small effective size of viral population hampers the use of conventional methods to calculate summary statistics. Here, we define statistics that overcome this problem by correcting for the sampling-time difference in quantifying a pairwise sequence difference. A simple linear regression method jointly estimates the mutation rate and the level of sequence polymorphism, thus providing an estimate of the effective population size. It also leads to the definition of Wright's FST for arbitrary time-series data. Furthermore, as an alternative to Tajima's D statistic or the site-frequency spectrum, a mismatch distribution corrected for sampling-time differences can be obtained and compared between actual and simulated data. Application of these methods to seasonal influenza A/H3N2 viruses sampled between 1980 and 2017 and sequences simulated under the model of recurrent positive selection with metapopulation dynamics allowed us to estimate the synonymous mutation rate and find parameter values for selection and demographic structure that fit the observation. We found that the mutation rates of HA and PB1 segments before 2007 were particularly high and that including recurrent positive selection in our model was essential for the genealogical structure of the HA segment. Methods developed here can be generally applied to population genetic inferences using serially sampled genetic data.
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Affiliation(s)
- Myriam Croze
- Division of EcoScience, Ewha Womans University, Seoul 03760, Korea
| | - Yuseob Kim
- Division of EcoScience, Ewha Womans University, Seoul 03760, Korea.,Department of Life Science, Ewha Womans University, Seoul 03760, Korea
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50
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Li X, Chen D, Zhang Y, Xue X, Zhang S, Chen M, Liu X, Ding G. Analysis of spatial-temporal distribution of notifiable respiratory infectious diseases in Shandong Province, China during 2005-2014. BMC Public Health 2021; 21:1597. [PMID: 34461855 PMCID: PMC8403828 DOI: 10.1186/s12889-021-11627-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 08/12/2021] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Little comprehensive information on overall epidemic trend of notifiable respiratory infectious diseases is available in Shandong Province, China. This study aimed to determine the spatiotemporal distribution and epidemic characteristics of notifiable respiratory infectious diseases. METHODS Time series was firstly performed to describe the temporal distribution feature of notifiable respiratory infectious diseases during 2005-2014 in Shandong Province. GIS Natural Breaks (Jenks) was applied to divide the average annual incidence of notifiable respiratory infectious diseases into five grades. Spatial empirical Bayesian smoothed risk maps and excess risk maps were further used to investigate spatial patterns of notifiable respiratory infectious diseases. Global and local Moran's I statistics were used to measure the spatial autocorrelation. Spatial-temporal scanning was used to detect spatiotemporal clusters and identify high-risk locations. RESULTS A total of 537,506 cases of notifiable respiratory infectious diseases were reported in Shandong Province during 2005-2014. The morbidity of notifiable respiratory infectious diseases had obvious seasonality with high morbidity in winter and spring. Local Moran's I analysis showed that there were 5, 23, 24, 4, 20, 8, 14, 10 and 7 high-risk counties determined for influenza A (H1N1), measles, tuberculosis, meningococcal meningitis, pertussis, scarlet fever, influenza, mumps and rubella, respectively. The spatial-temporal clustering analysis determined that the most likely cluster of influenza A (H1N1), measles, tuberculosis, meningococcal meningitis, pertussis, scarlet fever, influenza, mumps and rubella included 74, 66, 58, 56, 22, 64, 2, 75 and 56 counties, and the time frame was November 2009, March 2008, January 2007, February 2005, July 2007, December 2011, November 2009, June 2012 and May 2005, respectively. CONCLUSIONS There were obvious spatiotemporal clusters of notifiable respiratory infectious diseases in Shandong during 2005-2014. More attention should be paid to the epidemiological and spatiotemporal characteristics of notifiable respiratory infectious diseases to establish new strategies for its control.
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Affiliation(s)
- Xiaomei Li
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, No.619 Changcheng Road, Taian, 271016, Shandong Province, China
| | - Dongzhen Chen
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, No.619 Changcheng Road, Taian, 271016, Shandong Province, China.,Liaocheng Center for Disease Control and Prevention, Liaocheng, 252100, Shandong Province, China
| | - Yan Zhang
- Guiqian International General Hospital, Guiyang, 550018, Guizhou Province, China
| | - Xiaojia Xue
- Qingdao Municipal Center for Disease Control & Prevention, Qingdao, 266033, Shandong Province, China
| | - Shengyang Zhang
- Shandong Center for Disease control and Prevention, Jinan, 250014, Shandong Province, China
| | - Meng Chen
- Jining Center for Disease Control and Prevention, Qingdao, 272113, Shandong Province, China
| | - Xuena Liu
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, No.619 Changcheng Road, Taian, 271016, Shandong Province, China.
| | - Guoyong Ding
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, No.619 Changcheng Road, Taian, 271016, Shandong Province, China.
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