Molecular evolution of human influenza A viruses in a local area during eight influenza epidemics from 2000 to 2007

Molecular Characterization of Influenza A/H3N2 Virus Isolated from Indonesian Hajj and Umrah Pilgrims 2013 to 2014

The Hajj and Umrah are the annual mass gatherings of Muslims in Saudi Arabia and increase the transmission risk of acute respiratory infection. This study describes influenza infection among pilgrims upon arrival in Indonesia and the genetic characterization of imported influenza A/H3N2 virus. In total, 251 swab samples with influenza-like illness were tested using real-time RT-PCR for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and influenza viruses. Complete sequences of influenza A/H3N2 HA and NA genes were obtained using DNA sequencing and plotted to amino acid and antigenicity changes. Phylogenetic analysis was performed using a neighbour-joining method including the WHO vaccine strains and influenza A/H3N2 as references. The real-time RT-PCR test detected 100 (39.5%) samples positive with influenza with no positivity of MERS-CoV. Mutations in the HA gene were mainly located within the antigenic sites A, B, and D, while for the NA gene, no mutations related to oseltamivir resistance were observed. Phylogenetic analysis revealed that these viruses grouped together with clades 3C.2 and 3C.3; however, they were not closely grouped with the WHO-recommended vaccine (clades 3C.1). Sequences obtained from Hajj and Umrah pilgrims were also not grouped together with viruses from Middle East countries but clustered according to years of collection. This implies that the influenza A/H3N2 virus mutates continually across time.

Reconstruction of molecular evolution of human influenza A H1N1/2009 virus in Iran and neighboring countries

In this study, the time and path of transmission of H1N1 serotype influenza A viruses in Iran and neighboring countries have been investigated by using Bayesian phylogeography analysis on the sequences extracted from the gene bank. We obtained all hemagglutinin (HA) and neuraminidase (NA) nucleotide sequences of influenza H1N1 available up to December 25, 2020, from Iran and its neighboring countries (i.e., Pakistan, Afghanistan, Turkmenistan, Armenia, Azerbaijan, Turkey, and Iraq). We also performed a Bayesian Markov chain Monte Carlo method to infer the evolutionary dynamic and the most recent common ancestor for the HA and NA sequences. Based on the extracted sequences, the age of emergence of H1N1 influenza virus serotype was older in Iran compared to neighboring countries, and with some degree of uncertainty, it seems Tehran had a key role and epicenter of transmission to other cities within Iran. The mean time of the most recent common ancestor of H1N1 viruses was 1989 (95% HPD: 1980-1994) for HA and NA as well. Along with ordinary measures like resource management, diagnostic approaches, and preparedness to fight against viruses that were in place, continuous monitoring, and screening of H1N1 serotype influenza virus in the country, especially by implementation of feasible, effective, and innovative measures at borderline should be initiated and identified gaps and shortage that should be a priority for virus control. It is also important for countries to have a regional monitoring program in addition to internal monitoring programs, as well as to start a virus molecular care program.

Liu Shen Wan inhibits influenza a virus and excessive virus-induced inflammatory response via suppression of TLR4/NF-κB signaling pathway in vitro and in vivo

ETHNOPHARMACOLOGICAL RELEVANCE

Liu Shen Wan (LSW), first prescribed in "Lei Yunshang Song Fen Tang Fang", traditional Chinese medicine (TCM), is used to cure influenza, tonsillitis, pharyngitis and mumps for more than one hundred years.

AIM OF STUDY

LSW was proved extensive pharmacological properties, for instance, anti-inflammatory, anticancer, antiviral, analgesic, antibacterial and immunomodulatory activities. Nevertheless, the mechanism of this process and the evaluation of this product is still ambiguous. Hence, the study was designed to investigate the antiviral and anti-inflammatory activities of LSW against the influenza virus in vitro and vivo.

MATERIALS AND METHODS

The antiviral activities of LSW were assayed in virus-infected cells and mice. To study the antiviral effects of LSW against influenza A/PR/8/34 virus (PR8), we employed CPE inhibition assay with different concentrations of LSW at different times of infection in vitro. The mice were intranasally infected with virus to induce viral pneumonia, then treated with different doses of LSW. The death protection of the mice, the lung index, virus titer and pathological changes in the lung tissue of mice were investigated to estimate the anti-virus effect of LSW. Moreover, RT-qPCR was used to determine the mRNA expression of TNF-α, IL-1β, IL-6, and IFN-γ in the A549 cells and the supernatant of lung tissues, and the concentrations of these four cytokines in serum of mice were determined with ELISA. Western blot was used to determine the expression of TLR4, p-NF-κB p65, NF-κB p65, p-IκBα and IκBα in the A549 cells and lung tissues, which are the key targets of TLR4/NF-κB pathway. Moreover, the immunohistochemical assay was used to determine the expression of the NF-κB p65 in the mice lungs.

RESULTS

LSW could significantly inhibit influenza virus at different stages of viral replication (at the process of the pre-, post-, and co-virus infection) in vitro. And LSW (100 mg/kg and 50 mg/kg) could effectively increase the survival time of mice. The virus titres, lung index, pathological changes in the mice lungs also decreased. Moreover, LSW could significantly reduce the contents of IL-1β, TNF-α, IFN-γ and IL-6 in the infected cells and the infected-mice. In addition, LSW could significantly reduce the expression of TLR4, p-NF-κB p65, NF-κB p65 and p-IκBα, while increase the IκBα in the infected cells and in the lung of mice.

CONCLUSIONS

LSW could significantly not only inhibit virus replication and proliferation in vitro, but also ameliorate pneumonia damage in vivo. The antiviral effect was attributed to down-regulating the expression of inflammatory cytokines induced by influenza virus via regulating the activity of TLR4/NF-кB signaling pathway.

Antiviral effects and mechanisms of Yinhuapinggan granule against H1N1 influenza virus infection in RAW264.7 cells

Yinhuapinggan granule (YHPG), a modified prescription based on Ma-Huang-Tang (MHT), is used in traditional Chinese medicine (TCM) to treat influenza, cough, and viral pneumonia. In this study, we investigated the antiviral effects of YHPG by means of pre-, post-, and co-treatment, and its underlying mechanisms on regulating the levels of inflammatory-related cytokines, modulating the mRNA expressions of interferon-stimulated genes in influenza virus-infected murine macrophage cells (RAW264.7), and evaluating the protein expressions of key effectors in the Type I IFN and pattern recognition receptor (PRRs) signaling pathways. The results showed that YHPG markedly inhibited influenza virus (IFV) replication in pre-, post- and co-treatment assay, especially in post-treatment assay. Antiviral mechanisms studies revealed that YHPG (500 and 250 μg/mL) significantly up-regulated levels of IFN-β, IFN-stimulated genes (Mx-1, ISG-15 and ISG-56) compared with the IFV control group, while the levels of IL-6 and TNF-α were significantly down-regulated. Furthermore, western blot analysis results revealed that the protein expressions of the phosphorylated forms of TBK1, IRF3, ERK1/2, P38 MAPK and NF-κB p65 were significantly down-regulated in RAW264.7 cells with the YHPG (500 and 250 μg/mL) treatment, while the expression of the phosphorylated form of STAT1 was significantly enhanced. Based on these results, YHPG had antiviral effects in IFV-infected RAW264.7 cells, which might be associated with regulation of the inflammatory cytokines production, evaluation of the levels of IFN-stimulated genes, and modulation of the protein expressions of key effectors in the Type I IFN and PRRs signaling pathways.

Genetic diversity of the haemagglutinin (HA) of human influenza a (H1N1) virus in montenegro: Focus on its origin and evolution

In 2009 an influenza A epidemic caused by a swine origin H1N1strain, unusual in human hosts, has been described. The present research is aimed to perform the first phylogenetic investigation on the influenza virus A (H1N1) strains circulating in Montenegro, from December 1, 2009, when the first case of death due to H1N1 was confirmed, and the epidemic began causing a total of four fatalities. The phylogenetic analysis of the strains circulating showed the absence of a pure Montenegrin cluster, suggesting the occurrence of multiple re-introductions in that population from different areas till as far as the early 2010. The time to most recent common ancestor (TMRCA) for the complete dataset has been dated in early 2008, pre-dating the first Montenegrin identification of H1N1 infection. These data suggest that virus was spreading undetected, may be as a consequence of unidentified infections in returning travelers. Anyhow, the estimated TMRCA of Montenegrin strains is fully consistent to that found in different areas. Compatibly with the time coverage of the study period here analyzed, molecular dynamic of Montenegrin strains follows similar trend as in other countries. J. Med. Virol. 88:1905-1913, 2016. © 2016 Wiley Periodicals, Inc.

Full Genome Characterization of Human Influenza A/H3N2 Isolates from Asian Countries Reveals a Rare Amantadine Resistance-Conferring Mutation and Novel PB1-F2 Polymorphisms

Influenza A viruses evolve at a high rate requiring continuous monitoring to maintain the efficacy of vaccines and antiviral drugs. We performed next generation sequencing analysis of 100 influenza A/H3N2 isolates collected in four Asian countries (Japan, Lebanon, Myanmar, and Vietnam) during 2012-2015. Phylogenetic analysis revealed several reassortment events leading to the circulation of multiple clades within the same season. This was particularly evident during the 2013 and 2013/2014 seasons. Importantly, our data showed that certain lineages appeared to be fitter and were able to persist into the following season. The majority of A/H3N2 viruses continued to harbor the M2-S31N mutation conferring amantadine-resistance. In addition, an S31D mutation in the M2-protein, conferring a similar level of resistance as the S31N mutation, was detected in three isolates obtained in Japan during the 2014/2015 season. None of the isolates possessed the NA-H274Y mutation conferring oseltamivir-resistance, though a few isolates were found to contain mutations at the catalytic residue 151 (D151A/G/N or V) of the NA protein. These variations did not alter the susceptibility to neuraminidase inhibitors and were not detected in the original clinical specimens, suggesting that they had been acquired during their passage in MDCK cells. Novel polymorphisms were detected in the PB1-F2 open-reading frame resulting in truncations in the protein of 24-34 aminoacids in length. Thus, this study has demonstrated the utility of monitoring the full genome of influenza viruses to allow the detection of the potentially fittest lineages. This enhances our ability to predict the strain(s) most likely to persist into the following seasons and predict the potential degree of vaccine match or mismatch with the seasonal influenza season for that year. This will enable the public health and clinical teams to prepare for any related healthcare burden, depending on whether the vaccine match is predicted to be good or poor for that season.

Simultaneous and complete genome sequencing of influenza A and B with high coverage by Illumina MiSeq Platform

Active global surveillance and characterization of influenza viruses are essential for better preparation against possible pandemic events. Obtaining comprehensive information about the influenza genome can improve our understanding of the evolution of influenza viruses and emergence of new strains, and improve the accuracy when designing preventive vaccines. This study investigated the use of deep sequencing by the next-generation sequencing (NGS) Illumina MiSeq Platform to obtain complete genome sequence information from influenza virus isolates. The influenza virus isolates were cultured from 6 respiratory acute clinical specimens collected in Thailand and Nepal. DNA libraries obtained from each viral isolate were mixed and all were sequenced simultaneously. Total information of 2.6 Gbases was obtained from a 455±14 K/mm2 density with 95.76% (8,571,655/8,950,724 clusters) of the clusters passing quality control (QC) filters. Approximately 93.7% of all sequences from Read1 and 83.5% from Read2 contained high quality sequences that were ≥Q30, a base calling QC score standard. Alignments analysis identified three seasonal influenza A H3N2 strains, one 2009 pandemic influenza A H1N1 strain and two influenza B strains. The nearly entire genomes of all six virus isolates yielded equal or greater than 600-fold sequence coverage depth. MiSeq Platform identified seasonal influenza A H3N2, 2009 pandemic influenza A H1N1and influenza B in the DNA library mixtures efficiently.

Increased acid stability of the hemagglutinin protein enhances H5N1 influenza virus growth in the upper respiratory tract but is insufficient for transmission in ferrets

Influenza virus entry is mediated by the acidic-pH-induced activation of hemagglutinin (HA) protein. Here, we investigated how a decrease in the HA activation pH (an increase in acid stability) influences the properties of highly pathogenic H5N1 influenza virus in mammalian hosts. We generated isogenic A/Vietnam/1203/2004 (H5N1) (VN1203) viruses containing either wild-type HA protein (activation pH 6.0) or an HA2-K58I point mutation (K to I at position 58) (activation pH 5.5). The VN1203-HA2-K58I virus had replication kinetics similar to those of wild-type VN1203 in MDCK and normal human bronchial epithelial cells and yet had reduced growth in human alveolar A549 cells, which were found to have a higher endosomal pH than MDCK cells. Wild-type and HA2-K58I viruses promoted similar levels of morbidity and mortality in C57BL/6J mice and ferrets, and neither virus transmitted efficiently to naive contact cage-mate ferrets. The acid-stabilizing HA2-K58I mutation, which diminishes H5N1 replication and transmission in ducks, increased the virus load in the ferret nasal cavity early during infection while simultaneously reducing the virus load in the lungs. Overall, a single, acid-stabilizing mutation was found to enhance the growth of an H5N1 influenza virus in the mammalian upper respiratory tract, and yet it was insufficient to enable contact transmission in ferrets in the absence of additional mutations that confer α(2,6) receptor binding specificity and remove a critical N-linked glycosylation site. The information provided here on the contribution of HA acid stability to H5N1 influenza virus fitness and transmissibility in mammals in the background of a non-laboratory-adapted virus provides essential information for the surveillance and assessment of the pandemic potential of currently circulating H5N1 viruses.

Novel measurement of spreading pattern of influenza epidemic by using weighted standard distance method: retrospective spatial statistical study of influenza, Japan, 1999-2009

BACKGROUND

Annual influenza epidemics occur worldwide resulting in considerable morbidity and mortality. Spreading pattern of influenza is not well understood because it is often hampered by the quality of surveillance data that limits the reliability of analysis. In Japan, influenza is reported on a weekly basis from 5,000 hospitals and clinics nationwide under the scheme of the National Infectious Disease Surveillance. The collected data are available to the public as weekly reports which were summarized into number of patient visits per hospital or clinic in each of the 47 prefectures. From this surveillance data, we analyzed the spatial spreading patterns of influenza epidemics using weekly weighted standard distance (WSD) from the 1999/2000 through 2008/2009 influenza seasons in Japan. WSD is a single numerical value representing the spatial compactness of influenza outbreak, which is small in case of clustered distribution and large in case of dispersed distribution.

RESULTS

We demonstrated that the weekly WSD value or the measure of spatial compactness of the distribution of reported influenza cases, decreased to its lowest value before each epidemic peak in nine out of ten seasons analyzed. The duration between the lowest WSD week and the peak week of influenza cases ranged from minus one week to twenty weeks. The duration showed significant negative association with the proportion of influenza A/H3N2 cases in early phase of each outbreak (correlation coefficient was -0.75, P = 0.012) and significant positive association with the proportion of influenza B cases in the early phase (correlation coefficient was 0.64, P = 0.045), but positively correlated with the proportion of influenza A/H1N1 strain cases (statistically not significant). It is assumed that the lowest WSD values just before influenza peaks are due to local outbreak which results in small standard distance values. As influenza cases disperse nationwide and an epidemic reaches its peak, WSD value changed to be a progressively increasing.

CONCLUSIONS

The spatial distribution of nationwide influenza outbreak was measured by using a novel WSD method. We showed that spreading rate varied by type and subtypes of influenza virus using WSD as a spatial indicator. This study is the first to show a relationship between influenza epidemic trend by type/subtype and spatial distribution of influenza nationwide in Japan.

Xanthones from Polygala karensium inhibit neuraminidases from influenza A viruses

The emergence of the H1N1 swine flu pandemic has the possibility to develop the occurrence of disaster- or drug-resistant viruses by additional reassortments in novel influenza A virus. In the course of an anti-influenza screening program for natural products, 10 xanthone derivatives (1-10) were isolated by bioassay-guided fractionation from the EtOAc-soluble extract of Polygala karensium. Compounds 1, 3, 5, 7, and 9 with a hydroxy group at C-1 showed strong inhibitory effects on neuraminidases from various influenza viral strains, H1N1, H9N2, novel H1N1 (WT), and oseltamivir-resistant novel H1N1 (H274Y) expressed in 293T cells. In addition, these compounds reduced the cytopathic effect of H1N1 swine influenza virus in MDCK cells. Our results suggest that xanthones from P. karensium may be useful in the prevention and treatment of disease by influenza viruses.

Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community

BACKGROUND

There are few data in the literature on viral sequence variation between host generations/successive transmission events. Relatively little is known about the sequence heterogeneity of the influenza viruses transmitted within families.

OBJECTIVES

To study the molecular epidemiology of influenza virus and to determine the sequence variation within an individual, a household and a community during the first wave of influenza pandemic in 2009.

STUDY DESIGN

A prospective study of household transmission of influenza A in Hong Kong was conducted during the pandemic in 2009. The HA and NA sequences of pandemic and seasonal influenza A viral isolates identified in this household transmission study were sequences and analyzed.

RESULTS

Our results indicated that there were multiple introductions of influenza viruses into Hong Kong. Sequence analysis of these isolates suggested that members of these family clusters acquired the infection by household transmissions. Interestingly, unlike those concluded from previous household transmission studies, we observed sequence variations between sequential samples from the same person and also within the same household.

CONCLUSIONS

Family clusters of influenza A viral infection are predominantly the result of secondary transmission within a household. Our results also suggested that the intra-host viral sequence variation might be more common that than previously thought.

Molecular characteristics of outbreaks of nosocomial infection with influenza A/H3N2 virus variants

OBJECTIVE

To describe outbreaks of nosocomial influenza infection with molecular methods and to elucidate the viral linkages among outbreak case patients including both inpatients and healthcare workers (HCWs).

SETTING

A 180-bed acute and long-term care hospital in Japan.

METHODS

Retrospective observational study of nosocomial outbreaks of infection with influenza A/H3N2. Together with information about onset dates and vaccination history, we obtained nasopharyngeal swab samples from individuals with cases of influenza or influenza-like illness (ILI). The hemagglutinin genes of the recovered viruses were sequenced and compared, along with those of community-circulating strains, for similarity by phylogenetic tree analysis.

RESULTS

The outbreaks occurred from February 26 through April 3, 2007, during the 2006-2007 epidemic season, and they involved 11 patients and 13 HCWs. The 2 outbreaks involved 2 different genotypes of influenza A/H3N2 viruses. These virus variants were closely related to the influenza strains that were circulating in the community during the same epidemic season.

CONCLUSION

This study showed the dissemination of highly homologous influenza virus variants among inpatients and HCWs within a short period, as a result of nosocomial transmission. These strains were also similar to influenza strains that were circulating in the community.

Influenza emergence in the face of evolutionary constraints

Different influenza subtypes can evolve at very different rates, but the causes are not well understood. In this paper, we explore whether differences in transmissibility between subtypes can play a role if there are fitness constraints on antigenic evolution. We investigate the problem using a mathematical model that separates the interaction of strains through cross-immunity from the process of emergence for new antigenic variants. Evolutionary constraints are also included with antigenic mutation incurring a fitness cost. We show that the transmissibility of a strain can become disproportionately important in dictating the rate of antigenic drift: strains that spread only slightly more easily can have a much higher rate of emergence. Further, we see that the effect continues when vaccination is considered; a small increase in the rate of transmission can make it much harder to control the frequency at which new strains emerge. Our results not only highlight the importance of considering both transmission and fitness constraints when modelling influenza evolution, but may also help in understanding the differences between the emergence of H1N1 and H3N2 subtypes.

Evolutionary dynamics of the influenza A pandemic (H1N1) 2009 virus with emphasis on Indian isolates: evidence for adaptive evolution in the HA gene

The indigenous transmission of the 2009 pandemic H1N1 (pH1N1) virus in India made it as one of the major sub-types in circulation. Genetic characterization indicated that the viruses predominantly clustered in clade 7, the globally most widely circulating pH1N1 clade. It is imperative to continue monitoring the genetic make-up of the pH1N1 viruses to understand their adaptability and evolutionary dynamics in the country. We characterized 31 full genomes and 94 hemagglutinin (HA) sequences of the pH1N1 viruses from various regions of India (May 2009-October 2010). Among the newly identified mutations reported in the pH1N1 viruses that could alter the viral fitness, E374K in the HA was increasingly noted in 35 Indian isolates beyond September 2009 and its co-occurrence with D97N or V30A was also observed in the more recent isolates. Molecular clock analysis based on all Indian isolates and closely related global representatives indicated higher substitution rates (∼ 7.1 × 10(-3) subs/site/year) when compared to an earlier report. Several independent introductions were noted within the country along with considerable evidence of indigenous evolution during the latter period of the study. The estimate for the mean age of the common ancestor of all the pandemic isolates dated to around August 2008 correlating well with the global estimate. Evidence for adaptive evolution in the HA was observed in the clade 7 isolates at the 'Ca' antigenic site that may have implications for future re-evaluation of the vaccine composition. The study thus warrants the need for continued surveillance and genetic characterization of whole genome sequences to detect any possible reassortment events that might further contribute to the viral fitness of the pH1N1 viruses.

A novel sequence-based antigenic distance measure for H1N1, with application to vaccine effectiveness and the selection of vaccine strains

H1N1 influenza causes substantial seasonal illness and was the subtype of the 2009 influenza pandemic. Precise measures of antigenic distance between the vaccine and circulating virus strains help researchers design influenza vaccines with high vaccine effectiveness. We here introduce a sequence-based method to predict vaccine effectiveness in humans. Historical epidemiological data show that this sequence-based method is as predictive of vaccine effectiveness as hemagglutination inhibition assay data from ferret animal model studies. Interestingly, the expected vaccine effectiveness is greater against H1N1 than H3N2, suggesting a stronger immune response against H1N1 than H3N2. The evolution rate of hemagglutinin in H1N1 is also shown to be greater than that in H3N2, presumably due to greater immune selection pressure.

Dual resistance to adamantanes and oseltamivir among seasonal influenza A(H1N1) viruses: 2008-2010

Two distinct genetic clades of seasonal influenza A(H1N1) viruses have cocirculated in the recent seasons: clade 2B oseltamivir-resistant and adamantane-susceptible viruses, and clade 2C viruses that are resistant to adamantanes and susceptible to oseltamivir. We tested seasonal influenza A(H1N1) viruses collected in 2008-2010 from the United States and globally for resistance to antivirals approved by the Food and Drug Administration. We report 28 viruses with both adamantane and oseltamivir (dual) resistance from 5 countries belonging to 4 distinct genotypes. Because of limited options for antiviral treatment, emergence of dual-resistant influenza viruses poses a public health concern, and their circulation needs to be closely monitored.

C-Methylated Flavonoids from Cleistocalyx operculatus and Their Inhibitory Effects on Novel Influenza A (H1N1) Neuraminidase

As part of an ongoing study focused on the discovery of anti-influenza agents from plants, four new (1-4) and 10 known (5-14) C-methylated flavonoids were isolated from a methanol extract of Cleistocalyx operculatus buds using an influenza H1N1 neuraminidase inhibition assay. Compounds 4, 7, 8, and 14, with a chalcone skeleton, showed significant inhibitory effects on the viral neuraminidases from two influenza viral strains, H1N1 and H9N2. Compound 4 showed the strongest inhibitory activity against the neuraminidases from novel influenza H1N1 (WT) and oseltamivir-resistant novel H1N1 (H274Y mutant) expressed in 293T cells with IC50 values of 8.15 ± 1.05 and 3.31 ± 1.34 μM, respectively. Compounds 4, 7, 8, and 14 behaved as noncompetitive inhibitors in the kinetic studies. These results indicate that C-methylated flavonoids from C. operculatus have the potential to be developed as neuraminidase inhibitors for novel influenza H1N1.

Genomic events contributing to the high prevalence of amantadine-resistant influenza A/H3N2

BACKGROUND

The prevalence of amantadine-resistant influenza A/H3N2 viruses (belonging to the N-lineage), possessing an S31N mutation in the M2 protein and S193F and D225N substitutions in their HA1 subunit, has significantly increased worldwide since 2005. The aim of this study was to clarify the genomic events contributing to the evolution and continuity of the N-lineage amantadine-resistant viruses.

METHODS

The full genome sequence of A/H3N2 isolates, including both amantadine-resistant and amantadine-sensitive viruses, collected in Japan between 2006 and 2008, was determined and phylogenetically compared with isolates obtained from the database.

RESULTS

On the basis of the full genome sequence analysis, the N-lineage could be further divided into three genetically related clades: N1 (A/Wisconsin/67/2005-like amantadine-resistant viruses from years 2005-2007), N2 (amantadine-sensitive viruses from 2007) and N3 (A/Brisbane/10/2007-like amantadine-resistant viruses from 2007 and 2008). The 2006/2007 season showed cocirculation of antigenic variants of amantadine-resistant viruses of clades N1 and N3 in addition to the N2-sensitive viruses. In the 2007/2008 season, the clade N3 amantadine-resistant lineage dominated and replaced other strains. Phylogenetic analysis of each individual segment suggested that N2 and N3 were generated from two independent reassortment events involving clade N1 viruses and pre-N-lineage strains.

CONCLUSIONS

Our data show that several reassortment events have contributed to the evolution of amantadine-resistant A/H3N2 strains and, consequently, to the successful spread of this lineage. Although amantadine resistance is caused by single amino acid mutations in the M2 protein, genome-wide adjustment involving multiple genes appears to be necessary to obtain efficient replication and transmission of resistant viruses. Such adjustments are attainable through reassortment of segments among different virus lineages.

Antiviral drug susceptibilities of seasonal human influenza viruses in Lebanon, 2008-09 season

The emergence of antiviral drug-resistant strains of the influenza virus in addition to the rapid spread of the recent pandemic A(H1N1) 2009 virus highlight the importance of surveillance of influenza in identifying new variants as they appear. In this study, genetic characteristics and antiviral susceptibility patterns of influenza samples collected in Lebanon during the 2008-09 season were investigated. Forty influenza virus samples were isolated from 89 nasopharyngeal swabs obtained from patients with influenza-like illness. Of these samples, 33 (82.5%) were A(H3N2), 3 (7.5%) were A(H1N1), and 4 (10%) were B. All the H3N2 viruses were resistant to amantadine but were sensitive to oseltamivir and zanamivir; while all the H1N1 viruses were resistant to oseltamivir (possessed H275Y mutation, N1 numbering, in their NA) but were sensitive to amantadine and zanamivir. In the case of influenza B, both Victoria and Yamagata lineages were identified (three and one isolates each, respectively) and they showed decreased susceptibility to oseltamivir and zanamivir when compared to influenza A viruses. Influenza circulation patterns in Lebanon were very similar to those in Europe during the same season. Continued surveillance is important to fully elucidate influenza patterns in Lebanon and the Middle East in general, especially in light of the current influenza pandemic.

In silico genome analysis and drug efficacy test of influenza A virus (H1N1) 2009

The H1N1 2009 virus is pandemic in many countries. The genome of this virus contains eight segments. Among the eight segments maximum numbers of mutation occur at the segment 1 and segment 4 which codes for PB2 subunit and hemagglutinin (HA) and less number of mutations occur in segment 6 which codes for neuraminidase (NA) protein. Neuraminidase (NA) inhibitors (Oseltamivir and Zanamivir) are presently used as an anti-flu drugs. In the present study, the in silico efficacy of different drugs was tested against the swine flu virus. 3D structures of neuraminidase (NA) proteins of H1N1 2009 were generated using Geno3D. The 3D structure of H1N1 1918 was downloaded from PDB. Interaction study was done using Arguslab 4 and PyMol view. Oseltamivir and Zanamivir have good number of interactions with H1N1 2009 virus and the scoring function also support to this result. When compared with the 1918 H1N1 viral protein, 2009 H1N1 NA protein shows more number of interaction and good scoring function. The RMSD value of before and after docking are found to be same at 0.04A° for both the drugs. The force field energy of NA protein 2009 was found to be -15603.529 KJ/mol before docking. The force field energy was found to be decreased after docking at -17620.740 KJ/mol with Tamiflu and -17652.242 KJ/mol with Zanamivir. The number of interaction and scoring function shows that Oseltamivir and Zanamivir will be able to effectively control the present pandemic H1N1 virus 2009.

Loss of a single N-linked glycan from the hemagglutinin of influenza virus is associated with resistance to collectins and increased virulence in mice

Background

Glycosylation on the globular head of the hemagglutinin (HA) protein of influenza virus acts as an important target for recognition and destruction of virus by innate immune proteins of the collectin family. This, in turn, modulates the virulence of different viruses for mice. The role of particular oligosaccharide attachments on the HA in determining sensitivity to collectins has yet to be fully elucidated.

Methods

When comparing the virulence of H3N2 subtype viruses for mice we found that viruses isolated after 1980 were highly glycosylated and induced mild disease in mice. During these studies, we were surprised to find a small plaque variant of strain A/Beijing/353/89 (Beij/89) emerged following infection of mice and grew to high titres in mouse lung. In the current study we have characterized the properties of this small plaque mutant both in vitro and in vivo.

Results

Small plaque mutants were recovered following plaquing of lung homogenates from mice infected with influenza virus seed Beij/89. Compared to wild-type virus, small plaque mutants showed increased virulence in mice yet did not differ in their ability to infect or replicate in airway epithelial cells in vitro. Instead, small plaque variants were markedly resistant to neutralization by murine collectins, a property that correlated with the acquisition of an amino acid substitution at residue 246 on the viral HA. We present evidence that this substitution was associated with the loss of an oligosaccharide glycan from the globular head of HA.

Conclusion

A point mutation in the gene encoding the HA of Beij/89 was shown to ablate a glycan attachment site. This was associated with resistance to collectins and increased virulence in mice.