Organization of the Influenza A Virus Genomic RNA in the Viral Replication Cycle-Structure, Interactions, and Implications for the Emergence of New Strains

Influenza virus: Genomic insights, evolution, and its clinical presentation

Influenza viruses belong to the family Orthomyxoviridae and have been a concern for public health due to frequent epidemics and sporadic waves of pandemics. According to WHO, seasonal strains of the influenza A virus (IAV) infect 3 to 5 million people every year and result in 0.29-0.65 million deaths globally. Among all proteins of IAV, the hemagglutinin (HA) and neuraminidase (NA) have high mutation rates and have been reported to undergo antigenic drift and shift leading to novel strains. Hence continuous revision in drugs and vaccines regime is an economic burden as these reassortments can cause high morbidity among the immunologically naive population. Infection rates are higher among older age groups, infants and patients reported with other respiratory distress. Routine diagnostic tests include reverse transcription polymerase chain reaction (RT-PCR), viral culture, and immunofluorescence assays; however, the diagnosis may be hindered due to the resemblance of the clinical presentation of other respiratory viruses with influenza viruses. Here we present a comprehensive review which sheds light on the genomic structure, evolution, pathogenicity and clinical presentation of influenza virus that can help to distinguish it from other respiratory viruses. A detailed analysis will ultimately pave the way for the development of more effective antiviral drugs and a universal vaccine.

Emergence, migration and spreading of the high pathogenicity avian influenza virus H5NX of the Gs/Gd lineage into America

The high pathogenicity avian influenza virus H5N1, which first emerged in the winter of 2021, has resulted in multiple outbreaks across the American continent through the summer of 2023 and they continue based on early 2025 records, presenting significant challenges for global health and food security. The viruses causing the outbreaks belong to clade 2.3.4.4b, which are descendants of the lineage A/Goose/Guangdong/1/1996 (Gs/Gd) through genetic reassortments with several low pathogenicity avian influenza viruses present in populations of Anseriformes and Charadriiformes orders. This review addresses these issues by thoroughly analysing available epidemiological databases and specialized literature reviews. This project explores the mechanisms behind the resurgence of the H5N1 virus. It provides a comprehensive overview of the origin, timeline and factors contributing to its prevalence among wild bird populations on the American continent.

Raman signatures of type A and B influenza viruses: molecular origin of the "catch and kill" inactivation mechanism mediated by micrometric silicon nitride powder

A multiomic study of the structural characteristics of type A and B influenza viruses by means of highly spectrally resolved Raman spectroscopy is presented. Three virus strains, A H1N1, A H3N2, and B98, were selected because of their known structural variety and because they have co-circulated with variable relative prevalence within the human population since the re-emergence of the H1N1 subtype in 1977. Raman signatures of protein side chains tyrosine, tryptophan, and histidine revealed unequivocal and consistent differences for pH characteristics at the virion surface, while different conformations of two C-S bond configurations in gauche and trans methionine rotamers provided distinct low-wavenumber fingerprints for different virus lineages/subtypes. Short-term exposure to a few percent fraction of silicon nitride (Si3N4) micrometric powder in an aqueous environment completely inactivated the influenza virions, independent of lineage/subtype dependent characteristics. The molecular-scale details of the inactivation process were studied by Raman spectroscopy and interpreted in terms of a "catch and kill" mechanism, in which the hydrolyzing ceramic surface first attracts virions with high efficiency through electrochemical interactions (mimicking cellular sialic acid) and then "poisons" the viruses by local hydrolytic elution of ammonia and nitrogen radicals. The latter event causes severe damage to the virions' structures, including structural degradation of RNA purines, rotameric scrambling of methionine residues, formation of sulfhydryl and ionized carboxyl groups, and deprotonation/torsional deformation of tyrosine, tryptophan, and histidine residues. This study confirmed the antiviral effectiveness of Si3N4 powder, which is safe to the human body and simply activated by water molecules. Raman spectroscopy was confirmed as a powerful tool in molecular virology, complementary to genomics and unique in providing direct information on virus structures at the molecular scale.

In vivo secondary structural analysis of Influenza A virus genomic RNA

Influenza A virus (IAV) is a respiratory virus that causes epidemics and pandemics. Knowledge of IAV RNA secondary structure in vivo is crucial for a better understanding of virus biology. Moreover, it is a fundament for the development of new RNA-targeting antivirals. Chemical RNA mapping using selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) coupled with Mutational Profiling (MaP) allows for the thorough examination of secondary structures in low-abundance RNAs in their biological context. So far, the method has been used for analyzing the RNA secondary structures of several viruses including SARS-CoV-2 in virio and in cellulo. Here, we used SHAPE-MaP and dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) for genome-wide secondary structure analysis of viral RNA (vRNA) of the pandemic influenza A/California/04/2009 (H1N1) strain in both in virio and in cellulo environments. Experimental data allowed the prediction of the secondary structures of all eight vRNA segments in virio and, for the first time, the structures of vRNA5, 7, and 8 in cellulo. We conducted a comprehensive structural analysis of the proposed vRNA structures to reveal the motifs predicted with the highest accuracy. We also performed a base-pairs conservation analysis of the predicted vRNA structures and revealed many highly conserved vRNA motifs among the IAVs. The structural motifs presented herein are potential candidates for new IAV antiviral strategies.

Structural and Functional RNA Motifs of SARS-CoV-2 and Influenza A Virus as a Target of Viral Inhibitors

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic, whereas the influenza A virus (IAV) causes seasonal epidemics and occasional pandemics. Both viruses lead to widespread infection and death. SARS-CoV-2 and the influenza virus are RNA viruses. The SARS-CoV-2 genome is an approximately 30 kb, positive sense, 5' capped single-stranded RNA molecule. The influenza A virus genome possesses eight single-stranded negative-sense segments. The RNA secondary structure in the untranslated and coding regions is crucial in the viral replication cycle. The secondary structure within the RNA of SARS-CoV-2 and the influenza virus has been intensively studied. Because the whole of the SARS-CoV-2 and influenza virus replication cycles are dependent on RNA with no DNA intermediate, the RNA is a natural and promising target for the development of inhibitors. There are a lot of RNA-targeting strategies for regulating pathogenic RNA, such as small interfering RNA for RNA interference, antisense oligonucleotides, catalytic nucleic acids, and small molecules. In this review, we summarized the knowledge about the inhibition of SARS-CoV-2 and influenza A virus propagation by targeting their RNA secondary structure.

Recent Progress in Recombinant Influenza Vaccine Development Toward Heterosubtypic Immune Response

Flu, a viral infection caused by the influenza virus, is still a global public health concern with potential to cause seasonal epidemics and pandemics. Vaccination is considered the most effective protective strategy against the infection. However, given the high plasticity of the virus and the suboptimal immunogenicity of existing influenza vaccines, scientists are moving toward the development of universal vaccines. An important property of universal vaccines is their ability to induce heterosubtypic immunity, i.e., a wide immune response coverage toward different influenza subtypes. With the increasing number of studies and mounting evidence on the safety and efficacy of recombinant influenza vaccines (RIVs), they have been proposed as promising platforms for the development of universal vaccines. This review highlights the current progress and advances in the development of RIVs in the context of heterosubtypic immunity induction toward universal vaccine production. In particular, this review discussed existing knowledge on influenza and vaccine development, current hemagglutinin-based RIVs in the market and in the pipeline, other potential vaccine targets for RIVs (neuraminidase, matrix 1 and 2, nucleoprotein, polymerase acidic, and basic 1 and 2 antigens), and deantigenization process. This review also provided discussion points and future perspectives in looking at RIVs as potential universal vaccine candidates for influenza.

Increased virulence of a novel reassortant H1N3 avian influenza virus in mice as a result of adaptive amino acid substitutions

In this study, a novel multiple-gene reassortant H1N3 subtype avian influenza virus (AIV) (A/chicken/Zhejiang/81213/2017, CK81213) was isolated in Eastern China, whose genes were derived from H1 (H1N3), H7 (H7N3 and H7N9), and H10 (H10N3 and H10N8) AIVs. This AIV belongs to the avian Eurasian-lineage and exhibits low pathogenicity. Serial lung-to-lung passages of CK81213 in mice was performed to study the amino acid substitutions potentially related to the adaptation of H1 AIVs in mammals. And the mouse-adapted H1N3 virus showed greater virulence than wild-type H1N3 AIV in mice and the genomic analysis revealed a total of two amino acid substitutions in the PB2 (E627K) and HA (L67V) proteins. Additionally, the results of the animal study indicate that CK81213 could infect mice without prior adaption and become highly pathogenic to mice after continuous passage. Our findings show that routine surveillance of H1 AIVs is important for the prediction of influenza epidemics.

Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment

Influenza A virus (IAV) is a member of the single-stranded RNA (ssRNA) family of viruses. The most recent global pandemic caused by the SARS-CoV-2 virus has shown the major threat that RNA viruses can pose to humanity. In comparison, influenza has an even higher pandemic potential as a result of its high rate of mutations within its relatively short (<13 kbp) genome, as well as its capability to undergo genetic reassortment. In light of this threat, and the fact that RNA structure is connected to a broad range of known biological functions, deeper investigation of viral RNA (vRNA) structures is of high interest. Here, for the first time, we propose a secondary structure for segment 8 vRNA (vRNA8) of A/California/04/2009 (H1N1) formed in the presence of cellular and viral components. This structure shows similarities with prior in vitro experiments. Additionally, we determined the location of several well-defined, conserved structural motifs of vRNA8 within IAV strains with possible functionality. These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted. This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA level.

The Crossroads between Host Copper Metabolism and Influenza Infection

Three main approaches are used to combat severe viral respiratory infections. The first is preemptive vaccination that blocks infection. Weakened or dead viral particles, as well as genetic constructs carrying viral proteins or information about them, are used as an antigen. However, the viral genome is very evolutionary labile and changes continuously. Second, chemical agents are used during infection and inhibit the function of a number of viral proteins. However, these drugs lose their effectiveness because the virus can rapidly acquire resistance to them. The third is the search for points in the host metabolism the effect on which would suppress the replication of the virus but would not have a significant effect on the metabolism of the host. Here, we consider the possibility of using the copper metabolic system as a target to reduce the severity of influenza infection. This is facilitated by the fact that, in mammals, copper status can be rapidly reduced by silver nanoparticles and restored after their cancellation.

Conserved Structural Motifs of Two Distant IAV Subtypes in Genomic Segment 5 RNA

The functionality of RNA is fully dependent on its structure. For the influenza A virus (IAV), there are confirmed structural motifs mediating processes which are important for the viral replication cycle, including genome assembly and viral packaging. Although the RNA of strains originating from distant IAV subtypes might fold differently, some structural motifs are conserved, and thus, are functionally important. Nowadays, NGS-based structure modeling is a source of new in vivo data helping to understand RNA biology. However, for accurate modeling of in vivo RNA structures, these high-throughput methods should be supported with other analyses facilitating data interpretation. In vitro RNA structural models complement such approaches and offer RNA structures based on experimental data obtained in a simplified environment, which are needed for proper optimization and analysis. Herein, we present the secondary structure of the influenza A virus segment 5 vRNA of A/California/04/2009 (H1N1) strain, based on experimental data from DMS chemical mapping and SHAPE using NMIA, supported by base-pairing probability calculations and bioinformatic analyses. A comparison of the available vRNA5 structures among distant IAV strains revealed that a number of motifs present in the A/California/04/2009 (H1N1) vRNA5 model are highly conserved despite sequence differences, located within previously identified packaging signals, and the formation of which in in virio conditions has been confirmed. These results support functional roles of the RNA secondary structure motifs, which may serve as candidates for universal RNA-targeting inhibitory methods.