Phenotypic Drug Susceptibility Assay for Influenza Virus Neuraminidase Inhibitors

A flow cytometric (fluorescence-activated cell sorter [FACS]) assay was developed for analysis of the drug susceptibilities of wild-type and drug-resistant influenza A and B virus laboratory strains and clinical isolates for the neuraminidase (NA) inhibitors oseltamivir carboxylate, zanamivir, and peramivir. The drug susceptibilities of wild-type influenza viruses and those with mutations in the hemagglutinin (HA) and/or NA genes rendering them resistant to one or more of the NA inhibitors were easily determined with the FACS assay. The drug concentrations that reduced the number of virus-infected cells or the number of PFU by 50% as determined by the FACS assay were similar to those obtained with the more time-consuming and labor-intensive virus yield reduction assay. The NA inhibition (NAI) assay confirmed the resistance patterns demonstrated by the FACS and virus yield assays for drug-resistant influenza viruses with mutations in the NA gene. However, only the FACS and virus yield assays detected NA inhibitor-resistant influenza viruses with mutations in the HA gene but not in the NA gene. The FACS assay is more rapid and less labor-intensive than the virus yield assay and just as quantitative. The FACS assay determines the drug susceptibilities of influenza viruses with mutations in either the HA or NA genes, making the assay more broadly useful than the NAI assay for measuring the in vitro susceptibilities of influenza viruses for NA inhibitors. However, since only viruses with mutations in the NA gene that lead to resistance to the NA inhibitors correlate with clinical resistance, this in vitro assay should not be used in the clinical setting to determine resistance to NA inhibitors. The assay may be useful for determining the in vivo susceptibilities of other compounds effective against influenza A and B viruses.     

Neuraminidase inhibitor susceptibility of swine influenza A viruses isolated in Germany between 1981 and 2008

European swine influenza A viruses donated the matrix protein 2 as well as the neuraminidase (NA) gene to pandemic influenza A (H1N1) viruses that emerged in 2009. As a result, the latter became amantadine resistant and neuraminidase inhibitor (NAI) susceptible. These recent developments reflecting the close connection between influenza A virus infection chains in humans and pigs urge an antiviral surveillance within swine influenza A viruses. Here, NAI susceptibility of 204 serologically typed swine influenza A viruses of subtypes H1N1, H1N2, and H3N2 circulating in Germany between 1981 and 2008 was analyzed in chemiluminescence-based NA inhibition assays. Mean 50% inhibitory concentrations of oseltamivir and zanamivir indicate a good drug susceptibility of tested viruses. As found for human isolates, the oseltamivir and zanamivir susceptibility was subtype-specific. So, swine influenza A (H1N1) viruses were just as susceptible to oseltamivir as to zanamivir. In contrast, swine H1N2 and H3N2 influenza A viruses were more sensitive to oseltamivir than to zanamivir. Furthermore, reduction in plaque size and virus spread by both drugs was tested with selected H1N1 and H1N2 isolates in MDCK cells expressing similar amounts of α2.3- and α2.6-linked sialic acid receptors. Data obtained in cell culture-based assays for H1N1 isolates correlated with that from enzyme inhibition assays. But, H1N2 isolates that are additionally glycosylated at Asn158 and Asn163 near the receptor-binding site of hemagglutinin (HA) were resistant to both NAI in MDCK cells. Possibly, these additional HA glycosylations cause a misbalance between HA and NA function that hampers or abolishes NAI activity in cells.     

Monitoring of viral susceptibility: new challenges with the development of influenza NA inhibitors

With the clinical development of anti-viral agents, monitoring for the continued susceptibility of wild-type strains has become important in disease management. Various methods have been used to monitor viral susceptibility; the advantages and disadvantages of which depend on the virus, the target and the scale of the research being undertaken. The plaque-reduction assay is valuable for measuring susceptibility of most viruses but is not ideal for large-scale monitoring. Yield-reduction, measuring specific virus antigens, and dye-uptake assays, measuring virus cytopathic effects, are more suitable for high-throughput requirements, but the IC(50) value (the concentration that inhibits 50% of virus) varies with the viral inoculum. Surveillance of influenza susceptibility to rimantadine/amantadine in the clinic has predominantly used EIA-based assays, since plaquing of influenza clinical isolates is variable. With development of the influenza NA inhibitors it became apparent that current cell-based assays were unsuitable for monitoring susceptibility to this new class of drugs. Variability may result from virus spread directly from cell to cell in culture by-passing the NA function. Furthermore, mutations selected in the HA, while not apparently contributing to phenotypic resistance in vivo, may result in cell-culture based resistance, and may mask NA resistance in cell culture by modifying receptor-binding specificity. One important distinction between NA inhibitors and other antiviral enzyme inhibitors is that both target enzyme and inhibitor work extracellularly. NA assays are therefore most representative of the in vivo situation for monitoring susceptibility, supported by HA sequencing. As the clinical use of NA inhibitors escalates, a major change will be required in approaches used to monitor susceptibility of influenza isolates in virology laboratories world-wide.     

Rapid identification of neuraminidase inhibitor resistance mutations in seasonal influenza virus A(H1N1), A(H1N1)2009, and A(H3N2) subtypes by melting point analysis

The high mutation rate of influenza virus, combined with the increasing worldwide use of influenza virus-specific drugs, allows the selection of viruses that are resistant to the currently available antiviral medications. Therefore, reliable tests for the rapid detection of drug-resistant influenza virus strains are required. We evaluated the use of a procedure involving real-time polymerase chain reaction (PCR) followed by melting point analysis (MPA) of hybrids formed between the PCR product and a specific oligonucleotide probe for the identification of point mutations in the influenza A virus neuraminidase gene (NA) that are associated with oseltamivir resistance [resulting in the amino acid change H275Y for seasonal and pandemic influenza A(H1N1) viruses and E119V for A(H3N2) viruses]. Therefore, 54 seasonal A(H1N1) (12 oseltamivir-resistant and 42 sensitive strains), 222 A(H1N1)2009 (5 resistant, 217 sensitive), and 51 A(H3N2) viruses (2 resistant, 49 sensitive) were tested by MPA, and the results were compared to those obtained by sequencing the NA gene. The results clearly indicate that the identification of drug resistance mutations by MPA is as accurate as sequencing, irrespective of whether MPA is performed using clinical material or the corresponding isolate. MPA enables a clear identification of mutations associated with antiviral resistance.     

A new and rapid genotypic assay for the detection of neuraminidase inhibitor resistant influenza A viruses of subtype H1N1, H3N2, and H5N1

The neuraminidase of influenza viruses is the target of the inhibitors oseltamivir and zanamivir. Recent reports on influenza viruses with reduced susceptibility to neuraminidase inhibitors (NAI) are a cause for concern. Several amino acid substitutions, each as a consequence of one single nucleotide mutation, are known to confer resistance to NAI. An increase of NAI-resistant viruses appears to be likely as a result of a wider application of NAI for treatment and prophylaxis of seasonal influenza infections. Monitoring the occurrence and spread of resistant viruses is an important task. Therefore, RT-PCR assays were developed with subsequent pyrosequencing analysis (PSQ-PCR). These assays allow a rapid, high-throughput and cost-effective screening of subtype A/H1N1, A/H3N2, and A/H5N1 viruses. Various specimens such as respiratory swabs, allantoic fluid, or cell-propagated viruses can be used and results are available within hours. Several A/H1N1, A/H3N2, and A/H5N1 viruses isolated from human and avian specimens were tested to evaluate the method. Positive controls encoding resistance-associated mutations were created using site-directed mutagenesis. The results obtained with these controls showed that the assay can discriminate clearly the wild-type virus from a mutant virus. The detection limit of minor virus variants within the viral quasispecies amounts to 10%.     

Molecular mechanisms of influenza virus resistance to neuraminidase inhibitors

A wide use of inhibitors of influenza virus neuraminidase (NAIs) to control influenza in humans demands a better understanding of the mechanisms involved in the resistance emergence. In vitro studies demonstrate that both neuraminidase (NA) and hemagglutinin (HA) influence virus susceptibility to NAIs. Drug resistance conferred due to changes in the NA could be monitored in the NA inhibition assays. Zanamivir-selected viruses acquired the NA substitutions at residues 119 and 292; oseltamivir-selected--at 274 and 292; peramivir-selected--at 292; and A-315675-selected--at 119. The HA binding efficiency and therefore susceptibility to NAIs are affected by the amino acids forming the HA receptor-binding site, the location and number of oligosaccharide chains, and structure of the neuraminic acid-containing cellular receptors. The lack of suitable cell culture-based assays hampers the assessment of virus susceptibility in humans. Emergence of the viruses with the NAI-induced substitutions in the NA is uncommon in drug-treated humans, however a compromised state of the immune system promotes emergence of drug resistance. In vivo, the zanamivir-selected mutant contained a substitution at 152 (B/NA); the oseltamivir-selected mutants-at residues 119 (A/N2), 198 (B/NA), 274 (A/N1), and 292 (A/N2). Substitutions in the NA were often accompanied by impairment of virus infectivity and virulence in animal models. Because of complexity of mechanisms of virus resistance, further analysis of the viruses recovered from the drug-treated humans is warranted.     

Contribution of neuraminidase of influenza viruses to the sensitivity to serum inhibitors and reassortment efficiency

Live attenuated influenza vaccine (LAIV) consists of reassortant viruses with hemagglutinin (HA) and neuraminidase (NA) gene segments inherited from the circulating wild-type (WT) parental viruses and six internal protein-encoding gene segments from cold-adapted attenuated master donor viruses (genome composition 6 : 2). In this study, we describe the difficulties in development of LAIV strains depending on the phenotypic peculiarities of the WT viruses used for reassortment. Genomic-composition analysis of 849 reassortants revealed that over 80% of reassortants based on the inhibitor-resistant WT viruses inherited WT NA as compared to 26% of reassortants based on the inhibitor-sensitive WT viruses. In addition, the highest percentage of vaccine genotype reassortants was achieved when WT parental viruses were resistant to nonspecific serum inhibitors. We show that NA may play a role in the influenza virus’ sensitivity to a nonspecific serum inhibitors. Replacing the NA of the inhibitor-sensitive WT virus with the NA of the inhibitor-resistant master donor virus significantly decreased the sensitivity of the resulting reassortant virus to nonspecific inhibitors.     

Mutations of neuraminidase implicated in neuraminidase inhibitors resistance.

Influenza constitutes one of the most important upper respiratory tract infections regarding morbidity, and mortality. Prevention and treatment of influenza rely on inactivated vaccines and antiviral drugs. Zanamivir and Oseltamivir, the currently available influenza neuraminidase inhibitors (NAI) can be used in clinical practice for the treatment of influenza infection. These drugs have also shown their efficacy against highly pathogenic avian influenza. Recent transmission of avian H7N7 and H5N1 influenza virus to human emphasized the need for active antiviral against emerging influenza viruses. Since their introduction in clinical practice, numerous studies have been implemented to determine the rate of emergence of NAI resistant isolates. These studies describe mechanisms of resistance associated to mutations in the neuraminidase protein, and their consequence in virus fitness and transmission. This review is summarizing the mutations described in human and avian influenza neuraminidases that are associated to resistance or reduction in sensitivity.     

Influenza Antiviral Resistance Testing in New York and Wisconsin, 2006 to 2008: Methodology and Surveillance Data

The need for effective influenza antiviral susceptibility surveillance methods has increased due to the emergence of near-universal adamantane resistance in influenza A/H3N2 viruses during the 2005-2006 season and the appearance of oseltamivir resistance in the influenza A/H1N1 virus subtype during the 2007-2008 season. The two classes of influenza antivirals, the neuraminidase inhibitors (NAIs) and the adamantanes, are well characterized, as are many mutations that can confer resistance to these drugs. Adamantane resistance is imparted mainly by a S31N mutation in the matrix gene, while NAI resistance can result from a number of mutations in the neuraminidase gene. During the 2007-2008 season, a neuraminidase mutation (H274Y) conferring resistance to the NAI oseltamivir emerged worldwide in the A/H1N1 virus subtype. Surveillance methodology and data from New York (NY) and Wisconsin (WI) for the 2006-2007 and 2007-2008 influenza seasons are presented. We used an existing pyrosequencing method (R. A. Bright et al., Lancet 366:1175-1181, 2005) and a modified version of this method for detection of adamantane resistance mutations. For NAI resistance mutation detection, we used a mutation-specific pyrosequencing technique and developed a neuraminidase gene dideoxy sequencing method. Adamantane resistance in the A/H3N2 virus samples was 100% for 2007-2008, similar to the 99.8% resistance nationwide as reported by the CDC. Adamantane resistance was found in only 1.2% of NY and WI A/H1N1 virus samples, compared to that found in 10.8% of samples tested nationwide as reported by the CDC. Influenza A/H1N1 virus H274Y mutants were found in 11.1% of NY samples for 2007-2008, a level comparable to the 10.9% nationwide level reported by the CDC; in contrast, mutants were found in 17.4% of WI samples. These results indicate the need for regional influenza antiviral surveillance.Influenza virus is a highly contagious agent that can cause symptoms ranging from mild discomfort to severe respiratory disease and is a contributing factor in over 30,000 deaths annually in the United States alone (27). Currently, the major health-care strategies for controlling the spread of influenza entail two main approaches, vaccination and the use of antiviral drugs (21). Vaccines are the most effective method of limiting the spread of influenza and preventing symptoms (15). However, vaccine efficacy is limited to the strains selected for each year''s vaccine. Since vaccine development and production typically require several months, prediction of the major seasonal strains can be difficult and is occasionally inaccurate. Also, vaccination compliance can vary from year to year, and outbreaks in long-term-care facilities can occur regardless of the residents'' vaccination statuses. Thus, antiviral drugs may serve as the initial agents for the prevention and treatment of influenza. Currently, two classes of influenza antiviral drugs are approved for influenza prophylaxis and treatment in the United States: the M2 ion channel blockers (including amantadine and rimantadine, collectively referred to as the adamantanes) and the neuraminidase inhibitors (NAIs) (oseltamivir and zanamivir).Adamantanes are effective only against influenza type A virus; they function by blocking ion flow through the 97-amino-acid viral proton channel (the M2 protein of the matrix gene), which is necessary for replication (1). Adamantanes have been shown to be effective agents for the treatment of influenza symptoms as well as for prophylaxis (13, 23). However, recent publications have documented a rapid increase in the incidence of adamantane-resistant influenza virus strains during the 2005-2006 influenza season (4, 12). Adamantane resistance is associated with mutations in a short region of the M2 protein sequence encompassed in nucleotides 789 to 815 of the matrix gene. Thus far, five resistance mutations, in the codons for amino acids 26, 27, 30, 31, and 34, have been reported. The predominant circulating resistance mutation reported affects amino acid 31, resulting in a serine-to-asparagine (S31N) change (24, 26). During the 2005-2006 influenza season, the Centers for Disease Control and Prevention (CDC) found that more than 90% of A/H3N2 viruses circulating in the United States had the S31N adamantane resistance mutation and recommended that adamantanes not be used for treatment or prophylaxis of influenza until susceptibility can be reestablished (5). The results also indicated that only 4% of A/H1N1 viruses tested were adamantane resistant (12). In Asia during the same period, the levels of resistance were slightly higher: nearly all A/H3N2 and 15% of A/H1N1 viruses tested had an adamantane resistance mutation (12).The use of NAIs has increased as a result of the decreased efficacy of adamantanes against such a large proportion of circulating influenza viruses. NAI antivirals are analogues of sialic acid, the biological neuraminidase (NA) substrate. The NAIs disrupt viral replication by occupying the NA active site, thus limiting the binding of sialic acid and the subsequent NA cleavage of host cell receptors (21, 28). Although currently not as common as adamantane resistance, NAI resistance can develop as a result of amino acid-altering mutations in the NA gene of influenza virus. Characterized NAI resistance mutations, distributed throughout the NA gene, result in catalytic or structural changes that affect the sialic acid binding site. Several studies have developed models predicting that the increased use of NAI antivirals, such as during an influenza pandemic, may result in an increase in circulating NAI-resistant viruses, which could greatly decrease the overall efficacy of antivirals used in a pandemic situation (10, 20). In Japan, oseltamivir is often prescribed for prophylactic therapy, as well as for treatment of influenza cases. The widespread use of the drug has been cited as a reason for higher rates of resistance in Japan, previously found to be as high as 18% in pediatric cases (18). In the early part of the 2007-2008 influenza season, an oseltamivir-resistant A/H1N1 virus strain was reported first in Norway and subsequently in other countries worldwide (19, 29). In many European nations where oseltamivir use is very limited, a high percentage of the 2007-2008 influenza season''s A/H1N1 virus strains had the oseltamivir resistance mutation, H274Y. This finding may indicate that oseltamivir resistance can develop and spread, even in the absence of the selective pressure exerted by excessive use of the drug. Despite variable reports on the transmissibility of drug-resistant influenza viruses (3, 16), the H274Y mutant spread rapidly throughout Europe during the 2007-2008 season. Thus far, the oseltamivir-resistant virus has remained susceptible to zanamivir (7, 22).Clearly, timely and reliable methods are needed to monitor the development of resistance to influenza antivirals if these drugs are to be used effectively in both seasonal and pandemic situations. Here, we describe such methods for monitoring the mutations that are known to increase resistance to either adamantanes or NAIs. Pyrosequencing allows the rapid screening of the critical region of the influenza A virus matrix gene, for detection of specific adamantane resistance mutations, or of the NA gene, for detection of a specific NA resistance mutation (i.e., H274Y). For more-extensive NAI resistance genotypic analysis, a method that uses traditional Sanger sequencing and that is based on newly compiled databases of influenza virus sequences is described. We also report results, acquired with these methods, from surveillance programs conducted by two state public health laboratories during the 2006-2007 and 2007-2008 influenza seasons in New York (NY) and Wisconsin (WI).     

Application of three duplex real-time PCR assays for simultaneous detection of human seasonal and avian influenza viruses

This study was performed to develop real-time PCR (qPCR) for detection of human seasonal and avian influenza viruses in duplex format. First duplex qPCR detects haemagglutinin (HA) gene of influenza virus A(H1N1)pdm09 and HA gene of influenza virus A(H3N2), the second reaction detects neuraminidase (NA) gene of influenza virus A(H3N2) and NA gene of influenza virus A(H1N1)pdm09 and A(H5N1), and the third reaction detects HA gene of influenza A(H5N1) and nonstructural protein gene of influenza B virus. Primers and probes were designed using multiple alignments of target gene sequences of different reference strains. Assays were optimised for identical thermocycling conditions. Their specificity was confirmed by conventional PCR and monoplex qPCR with nucleic acids isolated from different influenza viruses and other respiratory pathogens. Plasmid constructs with a fragment of specific gene were used to assess sensitivity of the assay. The limit of detection ranged from 27 to 96 cDNA copies/reaction. Clinical specimens (n = 107) have been tested using new assays, immunofluorescence and monoplex qRT-PCR. It has been shown that developed assays have been capable of rapid and accurate simultaneous detection and differentiation of influenza viruses. They are more sensitive than immunofluorescence and at least as sensitive as monoplex qRT-PCR.     

Evaluation of influenza virus antiviral susceptibility testing in Europe: Results from the first external quality assessment exercise

BackgroundThe first antiviral susceptibility testing external quality assessment (EQA) was held for European influenza reference laboratories during winter 2010/11.ObjectivesTo assess European network influenza antiviral susceptibility testing capability and provide participants with an independent performance evaluation.Study designThe EQA panel contained ten coded specimens of inactivated human influenza A and B viruses with reduced susceptibility to neuraminidase inhibitors (NAI), or adamantanes. Twenty-four laboratories from 19 member states of the WHO European region analysed the panel using phenotypic (determination of 50% inhibitory concentration (IC₅₀) values by neuraminidase (NA) enzyme inhibition assay) and/or genotypic methods.ResultsAll 24 laboratories returned genotypic data for A(H1N1)pdm09 influenza virus, 18 (75%) for former seasonal A(H1N1), 16 (67%) for A(H3N2) and 15 (63%) for influenza B virus, correctly identifying NAI or adamantane reduced susceptibility-associated substitutions in the NA (mean 84%; range 52–100%) or M2 (mean 85%; range 73–94%), respectively. Thirteen laboratories (54%) returned phenotypic NAI susceptibility data. Despite inter-laboratory and inter-assay IC₅₀ value variation, all 13 laboratories correctly identified oseltamivir reduced susceptibility/resistance in pure preparations of A(H1N1) oseltamivir-resistant viruses. However, only 11 (85%) identified oseltamivir reduced susceptibility/resistance in a mixture of A(H1N1)pdm09 oseltamivir-sensitive/-resistant viruses. Furthermore, 3 laboratories (23%) considered oseltamivir-sensitive influenza B virus reduced susceptible/resistant.ConclusionsDetection of NA-H275Y in A(H1N1) viruses was achieved by most laboratories. IC₅₀ values and interpretation thereof varied for a sensitive/resistant virus mixture and for influenza B virus. The results of this exercise will assist harmonisation of antiviral susceptibility testing, interpretation and reporting within the European network through targeted training.     

Characterization of oseltamivir‐resistant influenza A(H1N1)pdm09 viruses in Taiwan in 2009–2011

The early isolated swine‐origin influenza A(H1N1)pdm09 viruses were susceptible to oseltamivir; however, there is a concern about whether oseltamivir‐resistant influenza A(H1N1)pdm09 viruses will spread worldwide as did the oseltamivir‐resistant seasonal influenza A(H1N1) viruses in 2007–2008. In this study, the frequency of oseltamivir resistance in influenza A(H1N1)pdm09 viruses was determined in Taiwan. From May 2009 to April 2011, 1,335 A(H1N1)pdm09‐positive cases in Taiwan were tested for the H275Y mutation in the neuraminidase (NA) gene that confers resistance to oseltamivir. Among these, 15 patients (1.1%) were found to be infected with H275Y virus. All the resistant viruses were detected after the patients have received the oseltamivir. The overall monthly ratio of H275Y‐harboring viruses ranged between 0% and 2.88%, and the peak was correlated with influenza epidemics. The genetic analysis revealed that the oseltamivir‐resistant A(H1N1)pdm09 viruses can emerged from different variants with a great diversity under drug pressure. The ratio of NA/HA activities in different clades of oseltamivir‐resistant viruses was reduced compared to those in the wild‐type viruses, indicating that the balance of NA/HA in the current oseltamivir‐resistant influenza A(H1N1)pdm09 viruses was interfered. It is possible that H275Y‐bearing A(H1N1)pdm09 virus has not yet spread globally because it lacks the essential permissive mutations that can compensate for the negative impact on fitness by the H275Y amino acid substitution in NA. Continuous monitoring the evolution patterns of sensitive and resistant viruses is required to respond to possible emergence of resistant viruses with permissive genetic background which enable the wide spread of resistance. J. Med. Virol. 85:379–387, 2013. © 2012 Wiley Periodicals, Inc.     

深圳市2008-2009年A型H1N1季节性流感病毒神经氨酸酶抑制剂耐药性监测

目的 对深圳市2008-2009年分离到的H1N1季节性流感病毒神经氨酸酶(NA)抑制剂的耐药性进行监测.方法 根据原始临床样本的采集时间,按周抽取了55株2008-2009年分离到的H1N1季节性流感病毒,对其NA片段进行全长测序,选取WHO推荐的疫苗株和部分国内外分离到的H1N1季节性流感病毒作为参考株,运用Mega3.1软件进行种系发生树的构建、耐药相关位点及糖基化位点的分析.结果 对NA片段的序列分析发现2008年有2株(7.1%)出现了H275Y突变,但是2009年则有25株(92.6%)出现了该突变.提示H275Y达菲耐药突变株成为了2009年深圳市社区传播的优势株.同时还发现了一株Q136K变异株,显示对乐感清出现耐药.分子进化分析结果显示,H275Y变异成为了毒株在系统进化树上分布的主要依据.所有的深圳株NA片段上潜在的糖基化位点序列保守.结论 大量H275Y达菲耐药株的出现提示在今后的工作中应当密切关注流感病毒的耐药进展,进一步加强其耐药机制的研究.

Abstract：

Objective To analyze neuraminidase(NA) inhibitor resistance of seasonal H1N1 influenza A viruses isolated in Shenzhen during 2008 to 2009. Methods The NA gene of these viruses were sequenced. Phylogenetic analysis of the sequences was performed with Mega3. 1 software. Results In 2008, most isolates of the seasonal H1 N1 virus were susceptible to neuraminidase inhibitors, but the H275Y mutation in the neuraminidase gene region associated with high-level oseltamivir resistance had been detected in 92.6% of the strains isolated in 2009. Furthermore, a strain with Q136K was found, which showed the resistance to Zanamivir. Conclusion In the light of emerging resistance, close monitoring and understanding of the nature and dynamics of resistance mutations in influenza virus should be a priority.     

Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014-2016 influenza seasons

In Cameroon, genome characterization of influenza virus has been performed only in the Southern regions meanwhile genetic diversity of this virus varies with respect to locality. The Northern region characterized by a Sudan tropical climate might have distinct genetic characterization. This study aimed to better understand the genetic diversity of influenza A(H3N2) viruses circulating in Northern Cameroon. Sequences of three gene segments (hemagglutinin (HA), neuraminidase (NA) and matrix (M) genes) were obtained from 16 A(H3N2) virus strains collected during the 2014 to 2016 influenza seasons in Garoua. The HA gene segments were analysed with respect to reference strains while the NA and M gene was analysed for reported genetic markers of resistance to antivirals. Analysis of the HA sequences revealed that majority of the virus strains grouped together with the 2016-2017 vaccine strain (3C.2a-A/Hong Kong/4801/2014) while 3/5 (60%) of the 2015 viral strains grouped together with the 2015-2016 vaccine strain 3C.3a-A/Switzerland/9715293/2013. Within clade 3C.2a, Northern Cameroon sequences mostly grouped in sub-clade A3 (10/16). Analysis of the coding regions of the NA and M genes showed that none had genetic markers of resistance to neuraminidase inhibitors but all strains possessed the S31N substitution of resistance to amantadine. Due to some discrepancies observed in this region with respect to the Southern regions of Cameroon, there is necessity of including all regions within a country in the sentinel surveillance of influenza. These data will enable to track changes in influenza viruses in Cameroon.     

Evolutionary changes in the NA and HA genes of H3N2 influenza virus in the Moscow Region during 2003-2009

During the winter 2009 outbreak in the Moscow Region, H3N2 influenza viruses were isolated from the nasopharyngeal washes of patients via their propagation in the human intestinal (Caco-2) and bronchial (Calu-3) epithelial cell cultures maintaining the proteolytic cleavage of HA0--> HA1+HA2 and multicycle virus replication. Analysis of the nucleotide sequences of virus RNA indicated that the 2009 viruses differed from those isolated in 2003 in 14 and 21 amino acids of the neuraminidase (NA) and hemagglutinin (HA) genes, respectively. The NA gene was 1762 nucleotides long whereas the 2003 isolates had a deletion of 66 nucleotides (22 amino acids) in the stalk region (short-stalk NA genotype) of viruses. The NA gene of the 2009 and 2003 isolates possessed an amino acid profile characterized for oseltamivir- and zanamivir-susceptible viral strains. The HA gene of the 2009 viruses contained an N-glycosylation site at Asn181 (an analog to Asn 65 numbering from a signal peptide), which correlated with the long-stalk NA gene. The 2009 viruses had Phe209 in the HA receptor binding center whereas the 2003 isolates possessed Ser209, which correlated with their differences in HA activity. Phylogenetic analysis showed that the NA genes of the 2003 and 2009 Moscow strains were located in the same genetic clade with a single common precursor while their HA genes were diverged in more genetic distance and located in different clades. Viral distribution in the phylogenetic tree indicated that the Moscow strains isolated in 2009 were not direct ancestors of those isolated in 2003; and during the period of 2003 to 2009, H3N2 influenza virus with a short-stalk NA genotype was substituted for a migrant virus possessing a long-stalk NA gene.     

Identification of a human influenza type B strain with reduced sensitivity to neuraminidase inhibitor drugs

A total of 126 influenza B isolates isolated between 1998 and 2002 from Australasia and the Asia-Pacific region were tested for their sensitivity to the neuraminidase (NA) inhibitor drugs zanamivir and oseltamivir carboxylate using a fluorescence-based enzyme assay. The mean (+/-1 S.D.) 50% inhibitory concentration (IC50) of the influenza B viruses tested was 1.41+/-0.53 nM against zanamivir and 14.91+/-14.31 nM with oseltamivir carboxylate. However, a single type B isolate (B/Perth/211/2001) from an infant who had not been treated with either of the NA inhibitor drugs, showed a nine-fold lower sensitivity to zanamivir and a 14-fold lower sensitivity to oseltamivir carboxylate compared with the mean IC50 of influenza B strains. A decrease in sensitivity to oseltamivir carboxylate and RWJ-270201 was also seen in both: a chemiluminescent assay and a second different fluorescent assay. Sequence analysis of the haemagglutinin HA1 region and the neuraminidase gene of B/Perth/211/2001 revealed no amino acid changes in sites that have previously been reported to confer resistance to either of the NAI drugs. Further investigations are in progress to identify the basis for this reduced sensitivity.     

Antiviral susceptibility profile of influenza A viruses; keep an eye on immunocompromised patients under prolonged treatment

There was an increase in severe and fatal influenza cases in Greece during the 2011–2015 post-pandemic period. To investigate causality, we determined neuraminidase (NA) inhibitor susceptibility and resistance-conferring NA and hemagglutinin (HA) mutations in circulating influenza type A viruses during the pandemic (2009–2010) and post-pandemic periods in Greece. One hundred thirty-four influenza A(H1N1)pdm09 and 95 influenza A(H3N2) viruses submitted to the National Influenza Reference Laboratory of Southern Greece were tested for susceptibility to oseltamivir and zanamivir. Antiviral resistance was assessed by neuraminidase sequence analysis, as well as the fluorescence-based 50 % inhibitory concentration (IC₅₀) method. Five influenza A(H1N1)pdm09 viruses (2.2 %) showed significantly reduced inhibition by oseltamivir (average IC₅₀ 300.60nM vs. 1.19nM) by Gaussian kernel density plot analysis. These viruses were isolated from immunocompromised patients and harbored the H275Y oseltamivir resistance-conferring NA substitution. All A(H1N1)pdm09 viruses were zanamivir-susceptible, and all A(H3N2) viruses were susceptible to both drugs. Oseltamivir-resistant viruses did not form a distinct cluster by phylogenetic analysis. Permissive mutations were detected in immunogenic and non immunogenic NA regions of both oseltamivir- resistant and susceptible viruses in the post-pandemic seasons. Several amino acid substitutions in the HA1 domain of the HA gene of post-pandemic viruses were identified. This study indicated low resistance to NAIs among tested influenza viruses. Antiviral resistance emerged only in immunocompromised patients under long-term oseltamivir treatment. Sequential sample testing in this vulnerable group of patients is recommended to characterise resistance or reinfection and viral evolution.     

High prevalence of amantadine-resistance influenza a (H3N2) in six prefectures, Japan, in the 2005-2006 season

Substantial increase in amantadine-resistant influenza A (H3N2) was reported in Asia and North America in 2005. In this study the frequency and genetic characteristics of amantadine-resistant influenza A, circulated in Japan in 2005-2006 season, were investigated. Isolates were tested by amantadine susceptibility test (TCID(50)/0.2 ml method), and sequencing of the M2 gene to identify mutations that confer resistance. Additionally, the hemagglutinin (HA) and neuraminidase (NA) genes of the viruses were examined. In total, 415 influenza A isolates from six prefectures were screened, and 231 (65.3%) of 354 influenza A (H3N2) were amantadine-resistant, with a serine to asparagine (S31N) change in the M2 gene. However, none of 61 A (H1N1) isolates were resistant. In addition, genetic analyses of the HA gene showed all amantadine-resistant viruses clustered in one (named clade N), possessing specific double mutations at 193, serine to phenylalanine (S193F), and at 225, asparatic acid to asparagine (D225N), and sensitive viruses belonged to another group (clade S). The clinical presentations at the clinical visit did not differ between patients shedding clade N virus and those shedding clade S virus. None of the patients had received previous treatment with amantadine. The results indicate an unusually high prevalence and wide circulation of the amantadine-resistance influenza A (H3N2) in Japan in the 2005-2006 season. These strains had the characteristic double mutations in the HA, in addition to the M2 mutation responsive for resistance. Antiviral resistance monitoring should be intensified and maintained for rapid feedback into treatment strategies, and selection of alternative therapeutic agents.     

H9N2禽流感病毒一步法双重荧光RT-PCR检测方法的建立

目的 建立一种可同时检测禽流感病毒H9N2的HA和NA基因一步法双重荧光RT-PCR方法.方法 针对H9N2禽流感病毒的HA和NA基因保守区,设计相应的特异性引物以及探针,优化检测体系及反应条件,建立一步法双重荧光定量RT-PCR方法.对该方法的灵敏度、特异性、稳定性进行验证与评估,并对家禽粪便标本进行应用检测,以单重实时荧光RT-PCR方法作为参照,检测结果不一致的样本采用测序进行验证.结果 该方法特异性强,与H1、H3、H5、H7亚型禽流感病毒、鸡新城疫及鸡传染性支炎病毒均无交叉反应,对HA和NA基因的最低检出限分别可达50拷贝/μL和25拷贝/μL,组间与组内的变异系数在0.20 ～0.79％之间.对82份粪便标本进行检测,H9N2禽流感病毒的阳性率为8.14％ (7/82),与单重实时荧光RT-PCR法检测结果一致.结论 该方法特异性强、灵敏度高、稳定性好,可应用于临床禽流感样本的检测.