Emergence and Genomic Characterisation of Influenza Virus A(H3N2) Subclade K in Saudi Arabia: Dominant Circulation With Fixed HA1 Substitutions and High‐Frequency HA–NA Clade Association, 2025–2026

Molecular Surveillance and Genomic Characterization of Influenza A(H3N2) Viruses From a Secondary‐Care Surveillance Site in Pakistan During the 2025–2026 Winter Season

Respiratory viral infections, particularly Influenza A and SARS‐CoV‐2, remain major public health concerns in endemic settings such as Pakistan, where high influenza‐like illness burden and limited genomic data underscore the need for surveillance to guide vaccine strategies. This study assessed respiratory virus circulation and genetic diversity among ILI cases at a secondary‐care hospital in Islamabad during the 2025–2026 winter season. Among 170 qRT‐PCR‐tested cases, Influenza A was detected in 24.1%, SARS‐CoV‐2 in 1.17%, and Influenza B was not detected. Influenza A positivity was slightly higher in females (25.0%), with highest burden in individuals aged 11–20 years. Whole‐genome sequencing of 21 Influenza A(H3N2) isolates revealed co‐circulation of subclade K (52.4%), J.2.2 (28.6%), and J.2 (9.5%). Phylogenetic analysis showed subclade K clustering with recent isolates from North America, Oceania, Europe, and WHO‐recommended 2026–2027 Northern Hemisphere H3N2 vaccine strains, whereas J.2 and J.2.2 aligned with earlier vaccine‐like strains. NA analysis showed predominance of clade B.4.2.2 associated with K‐lineage and relatedness to recent North American strains. Subclade K exhibited conserved HA substitutions (K2N, S144N, N158D, I160K, Q173R, T328A) and HA2 S49N with limited variation. No antiviral resistance mutations were detected. Overall, findings demonstrate predominance and genetic stability of H3N2 subclade K and support continuous genomic surveillance for vaccine strain selection and influenza preparedness.

Genomic Surveillance and Phylogenetic Analysis of Influenza A(H1N1) pdm09 and A(H3N2) Viruses in Burkina Faso, 2024

Background Influenza is a major cause of acute respiratory infections worldwide. In tropical regions such as Sub‐Saharan Africa, influenza circulates year‐round with irregular peaks, yet genomic data guiding prevention strategies remain limited. This study characterized the genetic diversity and seasonal dynamics of influenza A(H1N1)pdm09 and A(H3N2) viruses circulating in Burkina Faso in 2024. Methods A cross‐sectional study was conducted from January to December 2024, including seven sentinel surveillance sites. Patients presenting with influenza‐like illness or severe acute respiratory illness were enrolled. Respiratory specimens were tested by real‐time RT‐PCR. Influenza‐positive samples with a cycle threshold ≤ 30 underwent whole‐genome sequencing using Oxford Nanopore and Illumina platforms. Phylogenetic analyses and clade assignment were performed using MEGA Version 12. Results Out of 2951 samples tested, 6.74% were positive for influenza viruses. Females had higher odds of influenza positivity than males (OR = 1.48; 95% CI: 1.11–1.98). A significantly higher risk of positivity was observed in the age groups of 5–15 years (OR = 1.67; 95% CI: 1.07–2.52; p = 0.02) and 25–50 years (OR = 2.54; 95% CI: 1.53–4.03; p < 0.001). Influenza A(H3N2) peaked in July, while A(H1N1)pdm09 peaked in October. Phylogenetic analysis of 43 genomes revealed co‐circulation of multiple clades within both subtypes. Conclusion Influenza A viruses circulating in Burkina Faso in 2024 showed substantial genetic diversity, underscoring the need for continuous genomic surveillance to inform vaccine strain selection and public health strategies in tropical Africa.

Epidemiological, Clinical and Viral Genomic Features of Influenza Virus Infections Among Pilgrims During the Grand Magal of Touba Over 7 Years (2018–2024)

Large international gatherings such as the Grand Magal of Touba in Senegal may favor influenza A/B virus (IABV) transmission. We analyzed IABV genomes from human samples collected during the event in 2018–2024. Next‐generation sequencing was performed for 190 qPCR‐positive nasopharyngeal samples. Bioinformatic analyzes were performed using MAFFT v7.505, IQ‐TREE v2.2.0, iTOL, Nextclade, and PREDAV‐FluA. 106 (55.8%) complete genomes were obtained, including 99 type A and 7 type B. IAV genomes were classified as A/H3N2 (N = 48) and A/H1N1 (N = 43), based on hemagglutinin/neuraminidase‐encoding segments. A/H3N2 was not detected in 2021 and 2023; A/H1N1 was only detected in 2018, 2021 and 2023. Phylogenies classified A/H3N2 and A/H1N1 into distinct clades varying from 1 year to the next. A single A/H1N1 sequences was predicted to be antigenic divergence from the vaccine strain concomitantly used. All IBV genomes (clades V1A.3a or V1A.3a.2) were from 2020. Some IABV genomes from the GMT were clustered together while the most similar genomes from databases were from Senegal, Subsaharan Africa or other countries. Present data describes the circulation of IABV during the GMT over time in the population studied here shedding light on the viral dynamics in such setting of mass gathering.

The emergence of novel H3N8 and H3N3 avian influenza viruses in chickens during multi-province surveillance in China and their potential public health risk.

The H3 subtype avian influenza virus (AIV) poses a substantial global public health threat due to its high host adaptability and ongoing evolution. The recent emergence of novel H3N8 and H3N3 AIVs associated with cross-species transmission underscores the urgent need for enhanced epidemiological surveillance. In this study, we conducted surveillance and characterization of H3 AIVs based on a total of 737 poultry samples collected across 21 Chinese provinces from November 2022 to December 2023. Of these, 69 (9.4%) tested positive for H3 AIV by RT-qPCR, and one H3N8 isolate and ten H3N3 isolates were obtained for whole-genome characterization. We performed whole-genome sequencing, phylogenetic analysis, reassortment inference, and evaluation of key amino acid substitutions, alongside antigenic characterization using hemagglutination inhibition (HI) assays and an in vivo mouse challenge experiment. The H3N8 isolate was identified as a triple-reassortant virus possessing the Eurasian avian H3 gene, the North American avian N8 gene, and H9N2-derived internal genes. The H3N3 isolates represented reassortant viruses that had acquired the HA gene from the novel H3N8 AIV lineage, the NA gene from H10N3 AIV, and internal genes from H9N2 AIV. All isolates exhibited HA cleavage sites characteristic of low pathogenic avian influenza viruses. Additionally, several amino acid substitutions previously associated with enhanced mammalian adaptation were identified, including L89V and I292V in PB2 and H436Y in PB1. In a BALB/c mouse challenge experiment, the representative H3N8 virus established infection without prior adaptation and replicated predominantly in the upper respiratory tract, with detectable viral RNA in respiratory tissues and limited extrapulmonary dissemination. Antigenic analysis revealed no cross-reactivity between the novel H3 AIVs and H5, H7, or H9 AIVs as measured by HI. Based on molecular and phylogenetic characterization, antigenic assessment, and preliminary mammalian infection data, our findings provide evidence suggesting a potential public health risk. We recommend intensified surveillance of H3 AIVs in poultry and accelerated vaccine development to curb viral spread and improve public health preparedness.

Genomic characterization of H6N1 avian influenza viruses from wild birds and domestic ducks in the republic of Korea and Mongolia (2022–2024)

Detection and characterization of antiviral-resistant viruses during the influenza season of 2024–25

ABSTRACT During the high severity season of 2024–25, CDC with public health partners sequenced and analyzed genomes of >10,000 influenza viruses for antiviral resistance markers. Available sequence-flagged and representative viruses were tested with antivirals using in vitro assays. In the US, three oseltamivir-resistant A(H3N2) viruses had treatment-emergent neuraminidase (NA) mutations, either E119V or R292K. Oseltamivir-resistant A(H1N1)pdm09 viruses with NA-H275Y were detected in 15 states, albeit at a low frequency (0.53%). They belonged to several phylogenetic groups, with hemagglutinin (HA) subclade D.3.1 combined with either NA subclade D.1 or D.2 being most common. Based on shared sequence data, nearly all H275Y viruses from Australia, Canada, and Chile also belonged to these HA and NA subclades. Conversely, most H275Y viruses (68/81) from China belonged to HA subclade C.1.9 and NA subclade D and shared the permissive mutation R257K. Influenza polymerase acidic (PA) mutations conferring 4- to 92-fold decreased baloxavir susceptibility were detected in nine influenza A viruses. Viruses with PA-I38T showed mild attenuation of replicative fitness in three cell lines. Based on available data, NA-H275Y and PA-I38T viruses were collected from patients with no exposure to antivirals. Baseline susceptibility to all US-approved influenza antivirals remained largely unchanged compared to previous seasons. All swine-origin viruses detected in the US had adamantane resistance-conferring marker, M2-S31N, but remained susceptible to other approved antivirals. Monitoring antiviral susceptibility has substantially improved with increased sequencing capacities and bioinformatic support at public health laboratories. Information gained through influenza surveillance has been used to guide recommendations on antiviral use. IMPORTANCE Circulation of influenza viruses with reduced susceptibility to antivirals can diminish the usefulness of medications prescribed for influenza. This study informs on the prevalence of drug-resistant influenza viruses in the US during the high severity season of 2024–25. It provides information on susceptibility profile to all approved antiviral medications and on replicative fitness of representative drug-resistant viruses. Most drug-resistant viruses were collected from patients who were not exposed to antivirals indicating their ability to transmit from human to human. Whole-genome sequence (WGS)-based analysis is the cornerstone for surveillance, and numerous laboratories have been utilizing this approach. However, CDC laboratory is the only laboratory in the US conducting phenotypic testing of circulating viruses needed to confirm the outcomes of sequence-based analysis and to identify new molecular markers of resistance. Data gathered through virologic surveillance give much-needed information on drug susceptibility of influenza viruses which are used to guide recommendations on antiviral use. Circulation of influenza viruses with reduced susceptibility to antivirals can diminish the usefulness of medications prescribed for influenza. This study informs on the prevalence of drug-resistant influenza viruses in the US during the high severity season of 2024–25. It provides information on susceptibility profile to all approved antiviral medications and on replicative fitness of representative drug-resistant viruses. Most drug-resistant viruses were collected from patients who were not exposed to antivirals indicating their ability to transmit from human to human. Whole-genome sequence (WGS)-based analysis is the cornerstone for surveillance, and numerous laboratories have been utilizing this approach. However, CDC laboratory is the only laboratory in the US conducting phenotypic testing of circulating viruses needed to confirm the outcomes of sequence-based analysis and to identify new molecular markers of resistance. Data gathered through virologic surveillance give much-needed information on drug susceptibility of influenza viruses which are used to guide recommendations on antiviral use.