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Surface antigens of pathogens are commonly targeted by vaccine-elicited antibodies but antigenic variability, notably in RNA viruses such as influenza, HIV and SARS-CoV-2, pose challenges for control by vaccination. For example, influenza A(H3N2) entered the human population in 1968 causing a pandemic and has since been monitored, along with other seasonal influenza viruses, for the emergence of antigenic drift variants through intensive global surveillance and laboratory characterisation. Statistical models of the relationship between genetic differences among viruses and their antigenic similarity provide useful information to inform vaccine development though accurate identification of causative mutations is complicated by highly correlated genetic signals that arise due to the evolutionary process. Here, using a sparse hierarchical Bayesian analogue of an experimentally validated model for integrating genetic and antigenic data, we identify the genetic changes in influenza A(H3N2) virus that underpin antigenic drift. We show that incorporating protein structural data into variable selection helps resolve ambiguities arising due to correlated signals, with the proportion of variables representing haemagglutinin positions decisively included, or excluded, increased from 59.8% to 72.4%. The accuracy of variable selection judged by proximity to experimentally determined antigenic sites was improved simultaneously. Structure-guided variable selection thus improves confidence in the identification of genetic explanations of antigenic variation and we also show that prioritising the identification of causative mutations is not detrimental to the predictive capability of the analysis. Indeed, incorporating structural information into variable selection resulted in a model that could more accurately predict antigenic assay titres for phenotypically-uncharactrised virus from genetic sequence. Combined, these analyses have the potential to inform choices of reference viruses, the targeting of laboratory assays, and predictions of the evolutionary success of different genotypes, and can therefore be used to inform vaccine selection processes.

In the centenary year of the devastating 1918‐19 pandemic, it seems opportune to reflect on the success of the WHO Global Influenza Surveillance and Response System (GISRS) initiated 70 years ago to provide early warning of changes in influenza viruses circulating in the global population to help mitigate the consequences of such a pandemic and maintain the efficacy of seasonal influenza vaccines. Three pandemics later and in the face of pandemic threats from highly pathogenic zoonotic infections by different influenza A subtypes, it continues to represent a model platform for global collaboration and timely sharing of viruses, reagents and information to forestall and respond to public health emergencies.

It is more than 20 years since the neuraminidase inhibitors, oseltamivir and zanamivir were approved for the treatment and prevention of influenza. Guidelines for global surveillance and methods for evaluating resistance were established initially by the Neuraminidase Inhibitor Susceptibility Network (NISN), which merged 10 years ago with the International Society for influenza and other Respiratory Virus Diseases (isirv) to become the isirv-Antiviral Group (isirv-AVG). With the ongoing development of new influenza polymerase inhibitors and recent approval of baloxavir marboxil, the isirv-AVG held a closed meeting in August 2019 to discuss the impact of resistance to these inhibitors. Following this meeting and review of the current literature, this article is intended to summarize current knowledge regarding the clinical impact of resistance to polymerase inhibitors and approaches for surveillance and methods for laboratory evaluation of resistance, both in vitro and in animal models. We highlight limitations and gaps in current knowledge and suggest some strategies for addressing these gaps, including the need for additional clinical studies of influenza antiviral drug combinations. Lessons learned from influenza resistance monitoring may also be helpful for establishing future drug susceptibility surveillance and testing for SARS-CoV-2.

As avian influenza A(H5N1) viruses continue to circulate in Asia and Africa, global concerns of an imminent pandemic persist. Recent experimental studies suggest that efficient transmission between humans of current H5N1 viruses only requires a few genetic changes. An essential step is alteration of the virus hemagglutinin from preferential binding to avian receptors for the recognition of human receptors present in the upper airway. We have identified receptor-binding changes which emerged during H5N1 infection of humans, due to single amino acid substitutions, Ala134Val and Ile151Phe, in the hemagglutinin. Detailed biological, receptor-binding, and structural analyses revealed reduced binding of the mutated viruses to avian-like receptors, but without commensurate increased binding to the human-like receptors investigated, possibly reflecting a receptor-binding phenotype intermediate in adaptation to more human-like characteristics. These observations emphasize that evolution in nature of avian H5N1 viruses to efficient binding of human receptors is a complex multistep process., Highlights • Changes in receptor binding of HA during H5N1 human infection were identified. • Single A134V and L151F substitutions caused reduced affinity for avian receptors. • Glycan array analyses were used to identify changes in receptor binding specificity. • Structural basis for altered receptor binding was examined by X-ray crystallography.

Determining phenotype from genetic data is a fundamental challenge. Identification of emerging antigenic variants among circulating influenza viruses is critical to the vaccine virus selection process, with vaccine effectiveness maximized when constituents are antigenically similar to circulating viruses. Hemagglutination inhibition (HI) assay data are commonly used to assess influenza antigenicity. Here, sequence and 3-D structural information of hemagglutinin (HA) glycoproteins were analyzed together with corresponding HI assay data for former seasonal influenza A(H1N1) virus isolates (1997–2009) and reference viruses. The models developed identify and quantify the impact of eighteen amino acid substitutions on the antigenicity of HA, two of which were responsible for major transitions in antigenic phenotype. We used reverse genetics to demonstrate the causal effect on antigenicity for a subset of these substitutions. Information on the impact of substitutions allowed us to predict antigenic phenotypes of emerging viruses directly from HA gene sequence data and accuracy was doubled by including all substitutions causing antigenic changes over a model incorporating only the substitutions with the largest impact. The ability to quantify the phenotypic impact of specific amino acid substitutions should help refine emerging techniques that predict the evolution of virus populations from one year to the next, leading to stronger theoretical foundations for selection of candidate vaccine viruses. These techniques have great potential to be extended to other antigenically variable pathogens., Author Summary Influenza A viruses are characterized by rapid antigenic drift: structural changes in B-cell epitopes that facilitate escape from pre-existing immunity. Consequently, seasonal influenza continues to impose a major burden on human health. Accurate quantification of the antigenic impact of specific amino acid substitutions is a pre-requisite for predicting the fitness and evolutionary outcome of variant viruses. Using assays to attribute antigenic variation to amino acid sequence changes we identify substitutions that contribute to antigenic drift and quantify their impact. We show that substitutions identified as low-impact are a critical component of virus antigenic evolution and by including these, as well as the high-impact substitutions often focused on, the accuracy of predicting antigenic phenotypes of emerging viruses from genotype is doubled.

The plaque assay is a standard technique for measuring influenza virus infectivity and inhibition of virus replication. Counting plaque numbers and quantifying virus infection of cells in multiwell plates quickly, accurately and automatically remain a challenge. Visual inspection relies upon experience, is subjective, often time consuming, and has less reproducibility than automated methods. In this paper, a simple, high throughput imaging-based alternative is proposed which uses a flatbed scanner and image processing software to quantify the infected cell population and plaque formation. Quantitation results were evaluated with reference to visual counting and achieved better than 80% agreement. The method was shown to be particularly advantageous in titration of the number of plaques and infected cells when influenza viruses produce a heterogeneous population of small plaques. It was also shown to be insensitive to the densities of plaques in determination of neutralization titres and IC(50)s of drug susceptibility. In comparison to other available techniques, this approach is cost-effective, relatively accurate, and readily available.

Executive summary • For almost 60 years, the WHO Global Influenza Surveillance and Response System (GISRS) has been the key player in monitoring the evolution and spread of influenza viruses and recommending the strains to be used in human influenza vaccines. The GISRS has also worked to continually monitor and assess the risk posed by potential pandemic viruses and to guide appropriate public health responses.• The expanded and enhanced role of the GISRS following the adoption of the International Health Regulations (2005), recognition of the continuing threat posed by avian H5N1 and the aftermath of the 2009 H1N1 pandemic provide an opportune time to critically review the process by which influenza vaccine viruses are selected. In addition to identifying potential areas for improvement, such a review will also help to promote greater appreciation by the wider influenza and policy‐making community of the complexity of influenza vaccine virus selection.• The selection process is highly coordinated and involves continual year‐round integration of virological data and epidemiological information by National Influenza Centres (NICs), thorough antigenic and genetic characterization of viruses by WHO Collaborating Centres (WHOCCs) as part of selecting suitable candidate vaccine viruses, and the preparation of suitable reassortants and corresponding reagents for vaccine standardization by WHO Essential Regulatory Laboratories (ERLs).• Ensuring the optimal effectiveness of vaccines has been assisted in recent years by advances in molecular diagnosis and the availability of more extensive genetic sequence data. However, there remain a number of challenging constraints including variations in the assays used, the possibility of complications resulting from non‐antigenic changes, the limited availability of suitable vaccine viruses and the requirement for recommendations to be made up to a year in advance of the peak of influenza season because of production constraints.• Effective collaboration and coordination between human and animal influenza networks is increasingly recognized as an essential requirement for the improved integration of data on animal and human viruses, the identification of unusual influenza A viruses infecting human, the evaluation of pandemic risk and the selection of candidate viruses for pandemic vaccines.• Training workshops, assessments and donations have led to significant increases in trained laboratory personnel and equipment with resulting expansion in both geographical surveillance coverage and in the capacities of NICs and other laboratories. This has resulted in a significant increase in the volume of information reported to WHO on the spread, intensity and impact of influenza. In addition, initiatives such as the WHO Shipment Fund Project have facilitated the timely sharing of clinical specimens and virus isolates and contributed to a more comprehensive understanding of the global distribution and temporal circulation of different viruses. It will be important to sustain and build upon the gains made in these and other areas.• Although the haemagglutination inhibition (HAI) assay is likely to remain the assay of choice for the antigenic characterization of viruses in the foreseeable future, alternative assays – for example based upon advanced recombinant DNA and protein technologies – may be more adaptable to automation. Other technologies such as microtitre neuraminidase inhibition assays may also have significant implications for both vaccine virus selection and vaccine development.• Microneutralization assays provide an important adjunct to the HAI assay in virus antigenic characterization. Improvements in the use and potential automation of such assays should facilitate large‐scale serological studies, while other advanced techniques such as epitope mapping should allow for a more accurate assessment of the quality of a protective immune response and aid the development of additional criteria for measuring immunity.• Standardized seroepidemiological surveys to assess the impact of influenza in a population could help to establish well‐characterized banks of age‐stratified representative sera as a national, regional and global resource, while providing direct evidence of the specific benefits of vaccination.• Advances in high‐throughput genetic sequencing coupled with advanced bioinformatics tools, together with more X‐ray crystallographic data, should accelerate understanding of the genetic and phenotypic changes that underlie virus evolution and more specifically help to predict the influence of amino acid changes on virus antigenicity.• Complex mathematical modelling techniques are increasingly being used to gain insights into the evolution and epidemiology of influenza viruses. However, their value in predicting the timing and nature of future antigenic and genetic changes is likely to be limited at present. The application of simpler non‐mechanistic statistical algorithms, such as those already used as the basis of antigenic cartography, and phylogenetic modelling are more likely to be useful in facilitating vaccine virus selection and in aiding assessment of the pandemic potential of avian and other animal influenza viruses.• The adoption of alternative vaccine technologies – such as live‐attenuated, quadrivalent or non‐HA‐based vaccines – has significant implications for vaccine virus selection, as well as for vaccine regulatory and manufacturing processes. Recent collaboration between the GISRS and vaccine manufacturers has resulted in the increased availability of egg isolates and high‐growth reassortants for vaccine production, the development of qualified cell cultures and the investigation of alternative methods of vaccine potency testing. WHO will continue to support these and other efforts to increase the reliability and timeliness of the global influenza vaccine supply.• The WHO GISRS and its partners are continually working to identify improvements, harness new technologies and strengthen and sustain collaboration. WHO will continue in its central role of coordinating worldwide expertise to meet the increasing public health need for influenza vaccines and will support efforts to improve the vaccine virus selection process, including through the convening of periodic international consultations.

Neuraminidase (NA) inhibitors (NIs) are the first line of defense against influenza virus. Reverse genetics experiments allow the study of resistance mechanisms by anticipating the impacts of mutations to the virus. To look at the possibility of an increased effect on the resistance phenotype of a combination of framework mutations, known to confer resistance to oseltamivir or zanamivir, with limited effect on virus fitness, we constructed 4 viruses by reverse genetics in the A/Moscow/10/99 H3N2 background containing double mutations in their neuraminidase genes: E119D+I222L, E119V+I222L, D198N+I222L, and H274Y+I222L (N2 numbering). Among the viruses produced, the E119D+I222L mutant virus was not able to grow without bacterial NA complementation and the D198N+I222L mutant and H274Y+I222L mutant were not stable after passages in MDCK cells. The E119V+I222L mutant was stable after five passages in MDCK cells. This E119V-and-I222L combination had a combinatorial effect on oseltamivir resistance. The total NA activity of the E119V+I222L mutant was low (5% compared to that of the wild-type virus). This drop in NA activity resulted from a decreased NA quantity in the virion in comparison to that of the wild-type virus (1.4% of that of the wild type). In MDCK-SIAT1 cells, the E119V+I222L mutant virus did not present a replicative advantage over the wild-type virus, even in the presence of oseltamivir. Double mutations combining two framework mutations in the NA gene still have to be monitored, as they could induce a high level of resistance to NIs, without impairing the NA affinity. Our study allows a better understanding of the diversity of the mechanisms of resistance to NIs.

Four influenza pandemics have struck the human population during the last 100 years causing substantial morbidity and mortality. The pandemics were caused by the introduction of a new virus into the human population from an avian or swine host or through the mixing of virus segments from an animal host with a human virus to create a new reassortant subtype virus. Understanding which changes have contributed to the adaptation of the virus to the human host is essential in assessing the pandemic potential of current and future animal viruses. Here, we develop a measure of the level of adaptation of a given virus strain to a particular host. We show that adaptation to the human host has been gradual with a timescale of decades and that none of the virus proteins have yet achieved full adaptation to the selective constraints. When the measure is applied to historical data, our results indicate that the 1918 influenza virus had undergone a period of preadaptation prior to the 1918 pandemic. Yet, ancestral reconstruction of the avian virus that founded the classical swine and 1918 human influenza lineages shows no evidence that this virus was exceptionally preadapted to humans. These results indicate that adaptation to humans occurred following the initial host shift from birds to mammals, including a significant amount prior to 1918. The 2009 pandemic virus seems to have undergone preadaptation to human-like selective constraints during its period of circulation in swine. Ancestral reconstruction along the human virus tree indicates that mutations that have increased the adaptation of the virus have occurred preferentially along the trunk of the tree. The method should be helpful in assessing the potential of current viruses to found future epidemics or pandemics.

Nonhomogeneous Markov models of nucleotide substitution have received scant attention. Here we explore the possibility of using nonhomogeneous models to identify host shift nodes along phylogenetic trees of pathogens evolving in different hosts. It has been noticed that influenza viruses show marked differences in nucleotide composition in human and avian hosts. We take advantage of this fact to identify the host shift event that led to the 1918 'Spanish' influenza. This disease killed over 50 million people worldwide, ranking it as the deadliest pandemic in recorded history. Our model suggests that the eight RNA segments which eventually became the 1918 viral genome were introduced into a mammalian host around 1882-1913. The viruses later diverged into the classical swine and human H1N1 influenza lineages around 1913-1915. The last common ancestor of human strains dates from February 1917 to April 1918. Because pigs are more readily infected with avian influenza viruses than humans, it would seem that they were the original recipient of the virus. This would suggest that the virus was introduced into humans sometime between 1913 and 1918.

Co-expression of the BM2 protein with pH-sensitive HA reduces the conversion of HA to its low-pH conformation during transport to the cell surface in the same way as human M2 proteins. BM2 protein is capable of increasing vesicular pH by as much as 0.4 pH units. Mutation analysis showed that replacement of H19 in BM2 protein by A and L resulted in loss of activity, while M2, with the mutation H37A, remained active, but its severe toxicity was intolerable for cells. Whereas substitution of L or A for W23 abolished detectable activity of the BM2 channel, substitution of L for W41 in the M2 protein resulted in a functional ion channel but with reduced activity. W41 was not essential for functional activity of the M2 protein. Our results show some differences in the nature of the interaction of the histidine and tryptophan in the transmembrane domains of BM2 and M2 ion channels.

Correspondence: Dr Ruben O. Donis, Molecular Virology and Vaccines Branch, Influenza Division, NCIRD, Centers for Disease Control & Prevention, 1600 Clifton Road, NE, MS-G16, Atlanta, GA 30333, USA. Email: rvd6@cdc.gov Dr Gavin Smith, State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, Hong Kong SAR, China. E-mail: gjsmith@hku.hk *WHO ⁄OIE ⁄ FAO H5N1 Evolution Working Group members and collaborators can be found in the Appendix.

We studied the effects of a neuraminidase inhibitor (oseltamivir) and an inhibitor of influenza virus polymerases (ribavirin) against two highly pathogenic H5N1 influenza viruses. In vitro, A/Vietnam/1203/04 virus (clade 1) was highly susceptible to oseltamivir carboxylate (50% inhibitory concentration [IC50] = 0.3 nM), whereas A/Turkey/15/06 virus (clade 2.2) had reduced susceptibility (IC50= 5.5 nM). In vivo, BALB/c mice were treated with oseltamivir (1, 10, 50, or 100 mg/kg of body weight/day), ribavirin (37.5, 55, or 75 mg/kg/day), or the combination of both drugs for 8 days, starting 4 h before virus inoculation. Monotherapy produced a dose-dependent antiviral effect against the two H5N1 viruses in vivo. Three-dimensional analysis of the drug-drug interactions revealed that oseltamivir and ribavirin interacted principally in an additive manner, with several exceptions of marginal synergy or marginal antagonism at some concentrations. The combination of ribavirin at 37.5 mg/kg/day and oseltamivir at 1 mg/kg/day and the combination of ribavirin at 37.5 mg/kg/day and oseltamivir at 10 mg/kg/day were synergistic against A/Vietnam/1203/04 and A/Turkey/15/06 viruses, respectively. These optimal oseltamivir-ribavirin combinations significantly inhibited virus replication in mouse organs, prevented the spread of H5N1 viruses beyond the respiratory tract, and abrogated the cytokine response (P< 0.01). Importantly, we observed clear differences between the efficacies of the drug combinations against two H5N1 viruses: higher doses were required for the protection of mice against A/Turkey/15/06 virus than for the protection of mice against A/Vietnam/1203/04 virus. Our preliminary results suggest that oseltamivir-ribavirin combinations can have a greater or lesser antiviral effect than monotherapy, depending on the H5N1 virus and the concentrations used.

The 115 residue CM2 protein of influenza C virus is a structural homologue of the M2 protein of influenza A virus. Expression of the CM2 protein in Xenopus oocytes showed that it can form a voltage-activated ion channel permeable to Cl−. To investigate whether the CM2 protein has pH modulating activity comparable to that of the M2 protein, CM2 was co-expressed with a pH-sensitive haemagglutinin (HA) from influenza A virus. The results indicate that, like the M2 protein, the CM2 protein has a capacity to reduce the acidity of the exocytic pathway and reduce conversion of the pH-sensitive HA to its low pH conformation during transport to the cell surface. By contrast, the NB protein of influenza B virus has no detectable activity. Although, the pH modulating activity of the CM2 protein was substantially less than that of the M2 protein, these observations provide support for a role in virus uncoating analogous to that of M2.

Objectives The identification of antigenic variants and the selection of influenza viruses for vaccine production are based largely on antigenic characterisation of the haemagglutinin (HA) of circulating viruses using the haemagglutination inhibition (HI) assay. However, in addition to evolution related to escape from host immunity, variants emerging as a result of propagation in different cell substrates can complicate the interpretation of HI results. The objective was to develop further a micro-neutralisation (MN) assay to complement the HI assay in antigenic characterisation of influenza viruses to assess the emergence of new antigenic variants and reinforce the selection of vaccine viruses. Design and setting A 96-well-plate plaque reduction MN assay based on the measurement of infected cell population using a simple imaging technique. Sample Representative influenza A (H1N1) pdm09, A(H3N2) and B viruses isolated between 2004 and 2013 Main outcome measures and results Improvements to the plaque reduction MN assay included selection of the most suitable cell line according to virus type or subtype, and optimisation of experimental design and data quantitation. Comparisons of the results of MN and HI assays showed the importance of complementary data in determining the true antigenic relationships among recent human influenza A(H1N1)pdm09, A(H3N2) and type B viruses. Conclusions Our study demonstrates that the improved MN assay has certain advantages over the HI assay: it is not significantly influenced by the cell-selected amino acid substitutions in the neuraminidase (NA) of A(H3N2) viruses, and it is particularly useful for antigenic characterisation of viruses which either grow to low HA titre and/or undergo an abortive infection resulting in an inability to form plaques in cultured cells.

The influenza A virus M2 proton channel plays a role in two stages of virus replication. The proteins of two closely related strains of the avian H7 subtype of influenza A virus, Rostock and Weybridge, were found to differ in their pH-modulating activities and activation characteristics. Of three amino acid differences at residues 27, 38 and 44 within the membrane-spanning domain, substitution at residue 44 was necessary and sufficient to account for differences in trans-Golgi pH-modulating activity, whereas changes in all three were required to switch the activation characteristics of the Weybridge M2 to those of the Rostock M2. These results not only separate the two phenomena genetically, but also indicate that the ‘unique’ activation characteristics of the Rostock M2 channel were selected specifically. In addition, they point to the importance of functional complementarity between the activation characteristics of the M2 channel and the pH of membrane fusion by haemagglutinin during virus entry.

Evolution of influenza viruses involves both the gradual accumulation of mutations and genetic reassortment, due to the segmented nature of the RNA genome. Co-circulation of H1N1 and H3N2 viruses since 1977 provided the opportunity for reassortment between the subtypes. Although various reassortant viruses have circulated to limited extents, not until 2002 did H1N2 viruses, deriving an H1 from H1N1 viruses and seven genes from contemporary H3N2 viruses, become established worldwide. Following the re-emergence of B/Victoria/2/87-lineage viruses during 2001–2002, reassortants possessing a B/Victoria-lineage HA and B/Yamagata-lineage NA became the predominant B viruses circulating since the latter part of 2002. As well as demonstrating the role of reassortment in antigenic and genetic variation, these events provide further evidence of the limited divergence in the functional characteristics of HA and NA of distinct subtypes or lineages during the evolution of human influenza viruses.

The influenza A virus M2 protein as a proton-selective ion channel plays an important role in two steps of virus replication. Co-expression of the M2 protein with pH-sensitive HA reduces the conversion of HA to its low pH conformation during transport to the cell surface. Mutational analyses showed that replacement of Histidine 37 (His37) by Trp, Phe and Gln resulted in loss of activity. M2, with the mutation His37Ala, remained active but its severe toxicity is intolerable for cells. Whereas substitution of Ala for Trp 41 abolished detectable activity of the M2 channel, substitution of Leu resulted in a functional ion channel but with reduced activity. The activity of the Trp41Leu mutant M2, initially identified in a mutant virus, shows that the proposed role of tryptophan 41 in activation is not essential for functional activity.

In 1997, we were ill prepared to produce vaccines in response to the sudden emergence of highly pathogenic H5N1 influenza. This experience stimulated efforts to improve technical and regulatory procedures for pandemic vaccine virus development and, in February 2003, when highly pathogenic H5N1 influenza re-appeared in man, we were able to produce H5N1 vaccine strains by reverse genetics within the space of 3 months. The technical and regulatory progress which made this possible is reviewed and newly developed WHO biosafety risk assessment for vaccine production is described. Recommendations are made for the significant challenges that lie ahead.

The influenza A H1N1 viruses, initially isolated from pigs in Ireland in 1991, were genetically distinct from previously identified human and swine H1N1 viruses, and appear to be the result of introduction of an avian virus distinct from those circulating in pigs in other European countries. The first Irish H3N2 swine isolates were genetically closely related to human H3N2 viruses. In contrast, H3N2 viruses isolated during the latter half of the 1990s were reassortants possessing internal genes similar to those of the H1N1 viruses, and both subtypes acquired amantadine resistance. These changes mimic those which occurred among swine influenza viruses in continental Europe during the 1980s, and emphasize the apparent advantage of properties associated with the avian internal genes and amantadine resistance for maintenance of the viruses in pigs.

Studies of tryptophan fluorescence of purified influenza A virus M2 protein have identified two pH-dependent structural changes. (1) An increase in fluorescence on reduction of pH from 8 to 6 that involves tryptophan 15 within the N-terminal domain of the protein and may be associated with proton activation of the channel. (2) Quenching of the fluorescence of tryptophan 41 within the transmembrane domain of the channel by histidine 37 below pH 6 which is specifically reversed by drugs that block the M2 channel. The pH dependence of the latter effect, which monitors changes in the protonation of histidine 37, corresponds to that of proton current through the channel and provides evidence for the involvement of histidine 37 in proton permeation.

Influenza A H1N2 viruses, which emerged during 2001, are genetic reassortants between H1N1 and H3N2 subtype viruses which have cocirculated in the human population since 1977. They possess a H1 hemagglutinin antigenically and genetically similar to contemporary A/New Caledonia/20/99 (H1N1)-like viruses and seven genes closely related to those of recent A/Moscow/10/99 (H3N2)-like viruses. The viruses have spread to many regions of the world and have predominated over H1N1 viruses in several countries. Since half of the amino acid changes which accumulated in the HAs of H1N1 viruses since 1995 are in residues implicated in receptor binding, functional changes in the H1 HA may have facilitated its replacement of the H3 HA and may contribute to the future epidemiologic significance of these H1N2 viruses.

A novel conditional-lethal transgene system is defined in which a mutated influenza A virus ion-channel protein, which is permeable to monovalent cations, is lethal to cells on heterotypic expression and whose activity can be blocked by an antiviral drug (amantadine), is used to reversibly disrupt T-cell development. In vivo expression of the M2 ion channel, as a transgene under control of the T-cell specific p56(Lck) proximal promoter, resulted in total ablation of T-cell development with the accumulation of three distinct populations of early progenitor cells (CD44(+) CD25(-); CD44(+) CD25(+); CD44(+) CD25(hi)) in the thymic rudiment. In vitro development of transgenic fetal thymic progenitors to single-positive T cells could be rescued by antiviral drug treatment. Moreover, there was a radical reduction in B-cell lymphopoiesis, evident at the pre-B-cell stage, with a twofold increase of lymphoid cells 'in cycle' in transgenic bone marrow, indicative of major changes in haematopoietic homeostasis. This system may provide a generic protocol for conditional, lineage-specific cell ablation with available tissue-specific promoters for any eukaryotic developmental system, and provide a window on early T-cell development.

This review highlights the main points which emerged from the presentations and discussions at the 3rd isirv-Antiviral Group Conference - advances in clinical management. The conference covered emerging and potentially pandemic influenza viruses and discussed novel/pre-licensure therapeutics and currently approved antivirals and vaccines for the control of influenza. Current data on approved and novel treatments for non-influenza respiratory viruses such as MERS-CoV, respiratory syncytial virus (RSV) and rhinoviruses and the challenges of treating immunocompromised patients with respiratory infections was highlighted.

Recent intensive surveillance in Hong Kong resulted in the detection of two novel viruses in children during 1999—two cases of infection by an H9N2 avian virus in March and a single case of infection by an H3N2 swine virus in September. The two human H9N2 isolates are similar in antigenic and genetic characteristics to an H9N2 virus isolated from a quail in late 1997, but are antigenically distinct from other lineages of H9N2 viruses circulating in other species of birds as well as those isolated from pigs during 1998. It is likely, therefore, that as for the H5N1 viruses in 1997, these infections are the result of direct avian-to-human transmission. A striking similarity between the six internal genes of the H9N2 and H5N1 human isolates indicates that they are related by reassortment. The H3N2 virus A/HK/1774/99 is distinct from contemporary human H3N2 viruses and is similar in antigenic and genetic properties to H3N2 viruses recently circulating in pigs in Europe. Although the source of infection was not traced, the likely presence of similar viruses in pigs in Hong Kong has subsequently been confirmed. These two instances provide further evidence for the direct transfer of avian and swine viruses in causing human disease and highlights the potential for emergence, either by adaptation or genetic reassortment with a circulating human strain, of a novel human pathogen.

H3N2 and “avian-like” H1N1 subtypes have circulated in European pigs since the mid- to late 1970s. Following reassortment to acquire six internal genes of the H1N1 viruses in the early 1980s, the H3N2 viruses have evolved to produce antigenically distinguishable variants. Sw/Finistere/127/99, isolated from a pig in January 1999, was shown to be closely related in antigenic and genetic characteristics to contemporary human A/Sydney/5/97-like viruses, and may represent the emergence of another “human-like” virus in European pigs. The H1N1 viruses circulating in pigs in France have evolved gradually over the past 20 years, but are in general closely related to early isolates such as Sw/Finistere/2899/82. An antigenically distinct variant, represented by Sw/Ille et Vilaine/1455/99, represents a significant drift from other recent French H1N1 viruses. Most of the H1N2 reassortant viruses isolated in France and Italy since 1997 were shown to be genetically similar to the H1N2 viruses which have become prevalent in the U.K., but to exhibit significant variation in antigenicity. Genetic reassortment between H1N2 and H1N1 viruses has also contributed to the recent increase in diversity of viruses circulating in pigs in Europe, and emphasizes the potential difficulties in controlling influenza by vaccination. Since most of these swine viruses are resistant to amantadine, they provide an increasing pool of amantadine-resistant M genes for potential incorporation into future human viruses.

Objective. Due to the lack of correlation from 1994 to 1997 between the A H3N2 component of the influenza vaccine recommended for this period and the circulating viruses in Argentina, we decided to study the antigenic and genomic relationships of the 1998 A H3N2 Argentine circulating strains with the corresponding vaccine component for that year as recommended by the World Health Organization (WHO). Methods. We selected 18 influenza A H3N2 strains isolated in Argentina during 1998 to carry out an antigenic and genomic study of their hemagglutinin (HA) and neuraminidase (NA) proteins. For the genomic study we added 3 isolates from Uruguay. We compared the Argentine and Uruguayan strains with available reference strains. Results. We found that all 18 strains from Argentina were similar to the A/Sydney/5/97 (H3N2) strain, as opposed to the A/Wuhan/359/95 (H3N2) strain, which was the vaccine component. This result was confirmed by the genomic study. Conclusions. The approach that we applied in Argentina has improved the quality and quantity of information about influenza in the country. This type of work should be encouraged in other countries in order to help choose the most appropriate vaccine components each year and provide individuals with the best possible protection against influenza.

Objective. Due to the lack of correlation from 1994 to 1997 between the A H3N2 component of the influenza vaccine recommended for this period and the circulating viruses in Argentina, we decided to study the antigenic and genomic relationships of the 1998 A H3N2 Argentine circulating strains with the corresponding vaccine component for that year as recommended by the World Health Organization (WHO). Methods. We selected 18 influenza A H3N2 strains isolated in Argentina during 1998 to carry out an antigenic and genomic study of their hemagglutinin (HA) and neuraminidase (NA) proteins. For the genomic study we added 3 isolates from Uruguay. We compared the Argentine and Uruguayan strains with available reference strains. Results. We found that all 18 strains from Argentina were similar to the A/Sydney/5/97 (H3N2) strain, as opposed to the A/Wuhan/359/95 (H3N2) strain, which was the vaccine component. This result was confirmed by the genomic study. Conclusions. The approach that we applied in Argentina has improved the quality and quantity of information about influenza in the country. This type of work should be encouraged in other countries in order to help choose the most appropriate vaccine components each year and provide individuals with the best possible protection against influenza.Objetivos. Debido a la ausencia de correlación entre el componente A H3N2 de la vacuna antigripal recomendada para el período de 1994 a 1997 y los virus entonces circulantes en Argentina, se decidió estudiar las relaciones antigénicas y genómicas entre las cepas A H3N2 circulantes en Argentina en 1998 y el correspondiente componente de la vacuna recomendada para ese año por la Organización Mundial de la Salud. Métodos. Se seleccionaron 18 cepas de virus influenza A H3N2 aisladas en Argentina en 1998 y se efectuó un estudio antigénico y genómico de sus proteínas hemaglutinina (HA) y neuraminidasa (NA). En el estudio genómico también se investigaron 3 aislados procedentes de Uruguay. Las cepas argentinas y uruguayas se compararon con las cepas de referencia. Resultados. Se comprobó que las 18 cepas argentinas eran similares a la cepa A/ Sydney/5/97 (H3N2), y no a la cepa A/Wuhan/359/95 (H3N2), componente de la vacuna. El estudio genómico confirmó este resultado. Conclusiones. El método aplicado en este estudio ha mejorado cuantitativa y cualitativamente la información acerca de la influenza en Argentina. Se deberían alentar estudios de este tipo en otros países, con el fin de contribuir a la elección de los componentes más adecuados para la vacuna de cada año y proporcionar a los vacunados la mejor protección posible frente a la influenza.

Novel symmetrical nucIeotide-(5′,5′)-dimers of 3′-O-acetylthymidine, 3′-O-methylthymidine, 3′-O-ethylthymidine, 3′-O-n-propylthymidine and 3′-azido-3′-deoxythymidine (AZT) were synthesized as membrane soluble pro-drugs. These were prepared using phosphorodichloridate chemistry and were characterised by spectroscopic and analytical data. In-vitro evaluation of the derivatives in cells acutely infected with the human immunodeficiency virus (HIV-1) demonstrated a range of activities. These derivatives were generally found to display poor inhibition of HIV proliferation. Derivatives containing AZT moieties were found to be potent, but such compounds were less active than the parent nucleoside. The data indicated that the AZT-containing compounds act primarily via the release of the free nucleoside. However, in some cases, the dimers of certain inactive nucleoside analogues were found to be active. In these cases, release of the nucleoside alone cannot account for the activity.

We describe a convenient method for the synthesis of 5′-amino-3′-azido-3′,5′-dideoxythymidine, and its conversion to a 5′-blocked phosphate derivative. The compounds are evaluated as inhibitors of HIV-1 in vitro, but prove to be poorly effective by comparison to their 5′-oxygen analogues.

In the summer of 2003 in Jerusalem, Israel, 23 children were hospitalized with influenza A virus (A/Fujian/411/02-like virus) infection. The majority were neonates and infants. Clinical manifestations included neonatal fever, bronchitis, bronchiolitis, and pneumonia, and outcomes were favorable. Continued surveillance between epidemic seasons could allow early recognition of influenza strains that will appear in the following influenza season.

The inaugural conference of the Antiviral Group of the International Society for Influenza and other Respiratory Virus Diseases (ISIRV-AVG) was organised in conjunction with the Oswaldo Cruz Foundation (FIOCRUZ) in Rio de Janeiro, Brazil, in November 2011. The purpose of the meeting was to increase awareness of the antivirals available for combating influenza, of their efficacy and effectiveness in different situations, of policies for use against pandemic and seasonal influenza, and of the limitations posed by development of resistance ...

The fusion of virus and endosome membranes is an essential early stage in influenza virus infection. The low pH-induced conformational change which promotes the fusogenic activity of the haemagglutinin (HA) is thus an attractive target as an antiviral strategy. The anti-influenza drug Arbidol is representative of a class of antivirals which inhibits HA-mediated membrane fusion by increasing the acid stability of the HA. In this study two series of indole derivatives structurally related to Arbidol were designed and synthesized to further probe the foundation of its antiviral activity and develop the basis for a structure-activity relationship (SAR). Ethyl 5-(hydroxymethyl)-1-methyl-2-(phenysulphanylmethyl)-1. H-indole-3-carboxylate (15) was identified as one of the most potent inhibitors and more potent than Arbidol against certain subtypes of influenza A viruses. In particular, 15 exhibited a much greater affinity and preference for binding group 2 than group 1 HAs, and exerted a greater stabilising effect, in contrast to Arbidol. The results provide the basis for more detailed SAR studies of Arbidol binding to HA; however, the greater affinity for binding HA was not reflected in a comparable increase in antiviral activity of 15, apparently reflecting the complex nature of the antiviral activity of Arbidol and its derivatives.

The hemagglutinin (HA) of influenza A(H3N2) virus responsible for the 1968 influenza pandemic derived from an avian virus. On introduction into humans, its receptor binding properties had changed from a preference for avian receptors (α2,3-linked sialic acid) to a preference for human receptors (α2,6-linked sialic acid). By 2001, the avidity of human H3 viruses for avian receptors had declined, and since then the affinity for human receptors has also decreased significantly. These changes in receptor binding, which correlate with increased difficulties in virus propagation in vitro and in antigenic analysis, have been assessed by virus hemagglutination of erythrocytes from different species and quantified by measuring virus binding to receptor analogs using surface biolayer interferometry. Crystal structures of HA–receptor analog complexes formed with HAs from viruses isolated in 2004 and 2005 reveal significant differences in the conformation of the 220-loop of HA1, relative to the 1968 structure, resulting in altered interactions between the HA and the receptor analog that explain the changes in receptor affinity. Site-specific mutagenesis shows the HA1 Asp-225→Asn substitution to be the key determinant of the decreased receptor binding in viruses circulating since 2005. Our results indicate that the evolution of human influenza A(H3N2) viruses since 1968 has produced a virus with a low propensity to bind human receptor analogs, and this loss of avidity correlates with the marked reduction in A(H3N2) virus disease impact in the last 10 y.

Data on influenza in tropical and resource-limited countries are scarce. In this study we present results from 14 years of influenza surveillance in Senegal, one of the few tropical countries in Africa from which longitudinal data are available.From 1996 to 2009, we collected respiratory specimens from outpatients presenting with influenza-like illness at 13 facilities in order to investigate the epidemiology of seasonal influenza and the characteristics of the circulating influenza viruses. Specimens were tested for influenza using viral isolation and/or reverse-transcription polymerase chain reaction (RT-PCR).From 1996 to 2009, specimens were obtained from 9176 patients; 1233 (13%) were influenza-positive by virus isolation and/or RT-PCR. Among positive samples, 958 (77%) were influenza A, 268 (22%) influenza B, and 7 (1%) influenza type C; of influenza A viruses, 619 (65%) were A(H3) and 339 (35%) A(H1), of which 13 (1%) were identified as H1N2. The proportion positive was similar for children15 years, young adults 16-35 years, and adults 36-55 years (15%), but lower for persons55 years (9%). Although influenza A(H1), A(H3), and B all circulated during most years, influenza A(H3N2) predominated during 9 of the 14 years. Influenza activity consistently peaked during the rainy season (July-September). Phylogenetic analysis showed that viruses circulating in Senegal were similar to contemporary viruses circulating elsewhere in the world.Our data confirm that influenza is prevalent in Senegal, occurs in seasonal epidemics, and contributes to the burden of respiratory diseases in all age groups.

Two classes of antiviral drugs, neuraminidase inhibitors and adamantanes, are approved for prophylaxis and therapy against influenza virus infections. A major concern is that antiviral resistant viruses emerge and spread in the human population. The 2009 pandemic H1N1 virus is already resistant to adamantanes. Recently, a novel neuraminidase inhibitor resistance mutation I223R was identified in the neuraminidase of this subtype. To understand the resistance mechanism of this mutation, the enzymatic properties of the I223R mutant, together with the most frequently observed resistance mutation, H275Y, and the double mutant I223R/H275Y were compared. Relative to wild type, KM values for MUNANA increased only 2-fold for the single I223R mutant and up to 8-fold for the double mutant. Oseltamivir inhibition constants (KI) increased 48-fold in the single I223R mutant and 7500-fold in the double mutant. In both cases the change was largely accounted for by an increased dissociation rate constant for oseltamivir, but the inhibition constants for zanamivir were less increased. We have used X-ray crystallography to better understand the effect of mutation I223R on drug binding. We find that there is shrinkage of a hydrophobic pocket in the active site as a result of the I223R change. Furthermore, R223 interacts with S247 which changes the rotamer it adopts and, consequently, binding of the pentoxyl substituent of oseltamivir is not as favorable as in the wild type. However, the polar glycerol substituent present in zanamivir, which mimics the natural substrate, is accommodated in the I223R mutant structure in a similar way to wild type, thus explaining the kinetic data. Our structural data also show that, in contrast to a recently reported structure, the active site of 2009 pandemic neuraminidase can adopt an open conformation., Author Summary Recently, a pandemic A/H1N1 influenza virus was isolated from an immune compromised patient with a novel antiviral resistance pattern to the neuraminidase inhibitor class of drugs. This virus had an amino acid change in the viral neuraminidase enzyme; an isoleucine at position 223 was substituted by an arginine (I223R). Patients infected with such a virus leave physicians with reduced antiviral treatment options, since pandemic viruses are naturally resistant to the other class of antivirals, the adamantanes. Previously, we have shown that this mutant virus retains its potential to cause disease and may still be able to spread in the human population. Here we used enzyme kinetic measurements and crystal structures of the I223R mutant neuraminidase to determine the resistance mechanism of this amino acid change. We found that the I223R change results in shrinkage of the active site of the enzyme. As a result, binding of the neuraminidase inhibitors is affected. In addition, we found that the active site of our pandemic neuraminidase structure, crystallized in the absence of inhibitor, has an extra cavity (150-cavity) adjacent to the active site. Our study could aid in the development of novel inhibitors designed to target the 150-cavity and active site of the enzyme.

Novel alkyl hydrogen phosphonate derivatives of the anti-HIV nucleoside analogue AZT have been prepared by phosphorochloridite chemistry. These materials are designed to act as labile membrane-soluble prodrugs of the bioactive free nucleotides. In vitro evaluation has revealed the compounds to have a pronounced and selective antiviral action. Short-chain (C1-C7) alkyl derivatives are more potent than the parent hydrogen phosphonate, whilst one long-chain (C18) compound is less active. In an assay that demonstrates the toxicity of the parent drug AZT, the alkyl H-phosphonates appear to be less cytotoxic, whilst retaining full antiviral activity. Lastly, the compounds are all poorly active in a cell line (JM) that is poorly responsive to AZT, indicating that they act as depot forms of the nucleoside rather than of the free nucleotide.

The anti-influenza virus drug amantadine was shown to reduce the rate of fusion of liposomes with influenza A viruses whose replication is inhibited by this drug. The fusion with amantadine-resistant viruses was unaffected. Experiments with reassortant and mutant viruses showed that this effect was linked to the M2 protein and not to the haemagglutinin of the virus. The proton ionophore monensin, on the other hand, substantially increased the rate of fusion of the viruses tested. These results indicate that the kinetics of virus-liposome fusion can be modulated by the virus M2 protein, the target of amantadine action, and it is postulated that the M2 ion channel functions by transporting protons into the virion interior and facilitating virus uncoating.

International audience; Despite progress in our knowledge of the internal organisation of influenza virus particles, little is known about the determinants of their morphology and, more particularly, of the actual abundance of structural proteins at the virion level. To address these issues, we used cryo-EM to focus on viral (and host) factors that might account for observed differences in virion morphology and characteristics such as size, shape and glycoprotein (GP) spike density. Twelve recombinant viruses were characterised in terms of their morphology, neuraminidase activity and virus growth. The genomic composition was shown to be important in determining the GP spike density. In particular, polymerase gene segments and especially PB1/PB2 were shown to have a prominent influence in addition to that for HA in determining GP spike density, a feature consistent with a functional link between these virus components important for virus fitness.