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Dandachi I, Alrezaihi A, Amin D, AlRagi N, Alhatlani B, Binjomah A, Aleisa K, Dong X, Hiscox JA, Aljabr W. Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches. Microbiol Spectr 2024:e0066524. [PMID: 38904365 DOI: 10.1128/spectrum.00665-24] [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: 03/12/2024] [Accepted: 05/08/2024] [Indexed: 06/22/2024] Open
Abstract
Outbreaks of influenza A viruses are generally seasonal and cause annual epidemics worldwide. Due to their frequent reassortment and evolution, annual surveillance is of paramount importance to guide vaccine strategies. The aim of this study was to explore the molecular epidemiology of influenza A virus and nasopharyngeal microbiota composition in infected patients in Saudi Arabia. A total of 103 nasopharyngeal samples from 2015 and 12 samples from 2022 were collected from patients positive for influenza A. Sequencing of influenza A as well as metatranscriptomic analysis of the nasopharyngeal microbiota was conducted using Oxford Nanopore sequencing. Phylogenetic analysis of hemagglutinin, neuraminidase segments, and concatenated influenza A genomes was performed using MEGA7. Whole-genome sequencing analysis revealed changing clades of influenza A virus: from 6B.1 in 2015 to 5a.2a in 2022. One sample containing the antiviral resistance-mediating mutation S247N toward oseltamivir and zanamivir was found. Phylogenetic analysis showed the clustering of influenza A strains with the corresponding vaccine strains in each period, thus suggesting vaccine effectiveness. Principal component analysis and alpha diversity revealed the absence of a relationship between hospital admission status, age, or gender of infected patients and the nasopharyngeal microbial composition, except for the infecting clade 5a.2a. The opportunistic pathogens Staphylococcus aureus, Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis were the most common species detected. The molecular epidemiology appears to be changing in Saudi Arabia after the COVID-19 pandemic. Antiviral resistance should be carefully monitored in future studies. In addition, the disease severity of patients as well as the composition of the nasopharyngeal microbiota in patients infected with different clades should also be assessed.IMPORTANCEIn this work, we have found that the clade of influenza A virus circulating in Riyadh, KSA, has changed over the last few years from 6B.1 to 5a.2a. Influenza strains clustered with the corresponding vaccine strains in our population, thus emphasizing vaccine effectiveness. Metatranscriptomic analysis showed no correlation between the nasopharyngeal microbiome and the clinical and/or demographic characteristics of infected patients. This is except for the 5a.2a strains isolated post-COVID-19 pandemic. The influenza virus is among the continuously evolving viruses that can cause severe respiratory infections. Continuous surveillance of its molecular diversity and the monitoring of anti-viral-resistant strains are thus of vital importance. Furthermore, exploring potential microbial markers and/or dysbiosis of the nasopharyngeal microbiota during infection could assist in the better management of patients in severe cases.
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Affiliation(s)
- Iman Dandachi
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Abdulrahman Alrezaihi
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Dashty Amin
- Faculty of Health Sciences, Qaiwan International University, Sulaymaniyah, Kurdistan Region, Iraq
| | - Nurah AlRagi
- Pathology and Clinical Laboratory Medicine, King Fahad Medical City, Riyadh, Saudi Arabia
| | - Bader Alhatlani
- Department of Applied Medical Sciences, Unayzah Community College, Qassim University, Unayzah, Saudi Arabia
| | | | - Kholoud Aleisa
- Riyadh Regional Laboratory, Riyadh Ministry of Health, Riyadh, Saudi Arabia
| | - Xiaofeng Dong
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Julian A Hiscox
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
| | - Waleed Aljabr
- Research Center, King Fahad Medical City, Riyadh, Saudi Arabia
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, United Kingdom
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Caini S, Meijer A, Nunes MC, Henaff L, Zounon M, Boudewijns B, Del Riccio M, Paget J. Probable extinction of influenza B/Yamagata and its public health implications: a systematic literature review and assessment of global surveillance databases. THE LANCET. MICROBE 2024:S2666-5247(24)00066-1. [PMID: 38729197 DOI: 10.1016/s2666-5247(24)00066-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 05/12/2024]
Abstract
Early after the start of the COVID-19 pandemic, the detection of influenza B/Yamagata cases decreased globally. Given the potential public health implications of this decline, in this Review, we systematically analysed data on influenza B/Yamagata virus circulation (for 2020-23) from multiple complementary sources of information. We identified relevant articles published in PubMed and Embase, and data from the FluNet, Global Initiative on Sharing All Influenza Data, and GenBank databases, webpages of respiratory virus surveillance systems from countries worldwide, and the Global Influenza Hospital Surveillance Network. A progressive decline of influenza B/Yamagata detections was reported across all sources, in absolute terms (total number of cases), as positivity rate, and as a proportion of influenza B detections. Sporadically reported influenza B/Yamagata cases since March, 2020 were mostly vaccine-derived, attributed to data entry errors, or have yet to be definitively confirmed. The likelihood of extinction necessitates a rapid response in terms of reassessing the composition of influenza vaccines, enhanced surveillance for B/Yamagata, and a possible change in the biosafety level when handling B/Yamagata viruses in laboratories.
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Affiliation(s)
- Saverio Caini
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands.
| | - Adam Meijer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, Netherlands
| | - Marta C Nunes
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France; South African Medical Research Council, Vaccines & Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laetitia Henaff
- Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Malaika Zounon
- Center of Excellence in Respiratory Pathogens (CERP), Hospices Civils de Lyon, Lyon, France; Centre International de Recherche en Infectiologie, Team Public Health, Epidemiology and Evolutionary Ecology of Infectious Diseases, Université Claude Bernard 1, Inserm U1111, CNRS UMR5308, ENS de Lyon, Lyon, France
| | - Bronke Boudewijns
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands
| | - Marco Del Riccio
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands; Department of Health Sciences, University of Florence, Florence, Italy
| | - John Paget
- Netherlands Institute for Health Services Research (NIVEL), Utrecht, Netherlands
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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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