Genetic Diversity and Evolutionary Kinetics of Influenza A Virus H3N2 Subtypes Circulating in Riyadh, Saudi Arabia

Dudin, Gani Asa; Aziz, Ibrahim; Alzayed, Rasha M.; Ahmed, Anwar; Hussain, Tajamul; Somily, Ali M.; Alsaadi, Muslim M.; Almajhdi, Fahad N.

doi:10.3390/vaccines11030702

Cited by 3 publications

(2 citation statements)

References 37 publications

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“…Samples with a Ct value below 40 were considered positive for influenza virus. Additionally, the influenza‐positive samples were further subtyped using RT‐PCR test targeting for H3N2 and H1N1 9 …”

Section: Methodsmentioning

confidence: 99%

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Clinical, epidemiological, and genomic characteristics of a seasonal influenza A virus outbreak in Beijing: A descriptive study

Zhu,

2023

Journal of Medical Virology

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China experienced a severe influenza season that began at the end of February 2023. The aim of this post hoc analysis was to investigate the clinical, epidemiological, and genomic features of this outbreak in Beijing. The number of cases increased rapidly from the end of February and reached its peak in March, with 7262 confirmed cases included in this study. The median age was 33 years, and 50.3% of them were male. The average daily positive rate reached 69% during the peak period. The instantaneous reproduction number (Rt) showed a median of 2.1, exceeded 2.5 initially, and remaining above 1 for the following month. The most common symptoms were fever (75.0%), cough (51.0%), and expectoration (42.9%), with a median body temperature of 38.5°C (interquartile range 38–39). Eight clinical symptoms were more likely to be observed in cases with fever, with odds ratio greater than 1. Viral shedding time ranged from 3 to 25 days, with median of 7.5 days. The circulating viruses in Beijing mainly included H1N1pdm09 (clades 5a.2a and 5a.2a.1), following with H3N2 (clade 2a.2a.3a.1). The descriptive study suggests that influenza viruses in this influenza season had a higher transmissibility and longer shedding duration, with fever being the most common symptom.

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Section: Methodsmentioning

confidence: 99%

“…Additionally, the influenza-positive samples were further subtyped using RT-PCR test targeting for H3N2 and H1N1. 9…”

Section: Study Population and Sample Collectionmentioning

confidence: 99%

Clinical, epidemiological, and genomic characteristics of a seasonal influenza A virus outbreak in Beijing: A descriptive study

Zhu,

2023

Journal of Medical Virology

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Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches

Dandachi,

Alrezaihi,

Amin

et al. 2024

Microbiol Spectr

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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. IMPORTANCE In 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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Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase

Galeone,

Lee,

Monaghan

et al. 2024

Viruses

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Seasonal influenza viruses continuously evolve via antigenic drift. This leads to recurring epidemics, globally significant mortality rates, and the need for annually updated vaccines. Co-occurring mutations in hemagglutinin (HA) and neuraminidase (NA) are suggested to have synergistic interactions where mutations can increase the chances of immune escape and viral fitness. Association rule mining was used to identify temporal relationships of co-occurring HA–NA mutations of influenza virus A/H3N2 and its role in antigenic evolution. A total of 64 clusters were found. These included well-known mutations responsible for antigenic drift, as well as previously undiscovered groups. A majority (41/64) were associated with known antigenic sites, and 38/64 involved mutations across both HA and NA. The emergence and disappearance of N-glycosylation sites in the pattern of N-X-[S/T] were also identified, which are crucial post-translational processes to maintain protein stability and functional balance (e.g., emergence of NA:339ASP and disappearance of HA:187ASP). Our study offers an alternative approach to the existing mutual-information and phylogenetic methods used to identify co-occurring mutations, enabling faster processing of large amounts of data. Our approach can facilitate the prediction of critical mutations given their occurrence in a previous season, facilitating vaccine development for the next flu season and leading to better preparation for future pandemics.

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Genetic Diversity and Evolutionary Kinetics of Influenza A Virus H3N2 Subtypes Circulating in Riyadh, Saudi Arabia

Cited by 3 publications

References 37 publications

Clinical, epidemiological, and genomic characteristics of a seasonal influenza A virus outbreak in Beijing: A descriptive study

Clinical, epidemiological, and genomic characteristics of a seasonal influenza A virus outbreak in Beijing: A descriptive study

Molecular surveillance of influenza A virus in Saudi Arabia: whole-genome sequencing and metagenomic approaches

Evolutionary Insights from Association Rule Mining of Co-Occurring Mutations in Influenza Hemagglutinin and Neuraminidase

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