scholarly journals Graphical Method to Determine Sequence Variation on NA Protein of H5N1 Virus using Discrete Wavelet Transform

2021 ◽  
Vol 15 ◽  
pp. 161-165
Author(s):  
Shiwani Saini ◽  
Lillie Dewan
Keyword(s):  
Wavelet Transforms ◽  
Influenza A ◽  
H5n1 Virus ◽  
Influenza Pandemic ◽  
Antigenic Drift ◽  
Sequence Length ◽  
Discrete Wavelet ◽  
Genomic Information ◽  
Analysis Technique ◽  
Signal Processing Methods

Influenza A virus belongs to the Orthomyxoviridae family and its genome is divided in eight distinct linear segments of negative-sense single stranded ribonucleic acid (RNA). Of all the eight influenza protein sequences, mutations in hemagglutinin and neuraminidase proteins show significant variations in their sequences. The threat of Influenza pandemic is ever rising due to its constant antigenic drift. Thus there is a need to characterize the genomic information in these viruses and signal processing methods offer the advantage of faster analysis in comparison to conventional techniques. Genomic information is converted into digital form by representation of the nucleotide bases in the form of mathematical sequences. In this paper, sequence variations of H5N1 virus have been studied using wavelet transforms as a signal analysis technique. Nucleotide sequences of neuraminidase protein of influenza virus occurring in different regions, in different hosts and over different years have been downloaded from National Centre for Biotechnology Information (NCBI) database. Sequences are aligned and converted into mathematical sequences then transformed using wavelet transforms. Graphical representations of the transformed sequences have been used to localise the regions of mutations along the sequence length.

scholarly journals The European Union faces up to the threat of a pandemic: meeting at the DGV on the influenza A (H5N1) of the ad hoc group on communicable diseases Luxembourg 14 January 1998

1998 ◽  
Vol 3 (3) ◽  
pp. 25-6 ◽  
Author(s):  
J C Desenclos ◽  
R Manigat
Keyword(s):  
Influenza A ◽  
Case Fatality Rate ◽  
H5n1 Virus ◽  
Ad Hoc ◽  
Influenza Pandemic ◽  
Case Fatality ◽  
Fatality Rate ◽  
The European Union ◽  
High Case Fatality Rate ◽  
Influenza H5n1

The transmission of an avian influenza H5N1 virus to a child in Hong Kong in May 1997 followed by the occurrence of 17 other human cases with a high case fatality rate (6/18, 33%) suggested that an influenza pandemic could be imminent and led many Europea

scholarly journals Repositioning Drugs on Human Influenza A Viruses Based on a Novel Nuclear Norm Minimization Method

2021 ◽  
Vol 11 ◽  
Author(s):  
Hang Liang ◽  
Li Zhang ◽  
Lina Wang ◽  
Man Gao ◽  
Xiangfeng Meng ◽  
...  
Keyword(s):  
Influenza A ◽  
Chemical Structure ◽  
Cross Validation ◽  
Drug Repositioning ◽  
Influenza Pandemic ◽  
Protein Docking ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Nuclear Norm ◽  
Influenza A Viruses

Influenza A viruses, especially H3N2 and H1N1 subtypes, are viruses that often spread among humans and cause influenza pandemic. There have been several big influenza pandemics that have caused millions of human deaths in history, and the threat of influenza viruses to public health is still serious nowadays due to the frequent antigenic drift and antigenic shift events. However, only few effective anti-flu drugs have been developed to date. The high development cost, long research and development time, and drug side effects are the major bottlenecks, which could be relieved by drug repositioning. In this study, we proposed a novel antiviral Drug Repositioning method based on minimizing Matrix Nuclear Norm (DRMNN). Specifically, a virus-drug correlation database consisting of 34 viruses and 205 antiviral drugs was first curated from public databases and published literature. Together with drug similarity on chemical structure and virus sequence similarity, we formulated the drug repositioning problem as a low-rank matrix completion problem, which was solved by minimizing the nuclear norm of a matrix with a few regularization terms. DRMNN was compared with three recent association prediction algorithms. The AUC of DRMNN in the global fivefold cross-validation (fivefold CV) is 0.8661, and the AUC in the local leave-one-out cross-validation (LOOCV) is 0.6929. Experiments have shown that DRMNN is better than other algorithms in predicting which drugs are effective against influenza A virus. With H3N2 as an example, 10 drugs most likely to be effective against H3N2 viruses were listed, among which six drugs were reported, in other literature, to have some effect on the viruses. The protein docking experiments between the chemical structure of the prioritized drugs and viral hemagglutinin protein also provided evidence for the potential of the predicted drugs for the treatment of influenza.

scholarly journals Preparing intensive care for the next pandemic influenza

Critical Care ◽  
2019 ◽  
Vol 23 (1) ◽  
Author(s):  
Taylor Kain ◽  
Robert Fowler
Keyword(s):  
Resource Allocation ◽  
Influenza Virus ◽  
Intensive Care ◽  
Pandemic Influenza ◽  
Influenza A ◽  
Large Scale ◽  
Influenza Pandemic ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Timely Initiation

Abstract Few viruses have shaped the course of human history more than influenza viruses. A century since the 1918–1919 Spanish influenza pandemic—the largest and deadliest influenza pandemic in recorded history—we have learned much about pandemic influenza and the origins of antigenic drift among influenza A viruses. Despite this knowledge, we remain largely underprepared for when the next major pandemic occurs. While emergency departments are likely to care for the first cases of pandemic influenza, intensive care units (ICUs) will certainly see the sickest and will likely have the most complex issues regarding resource allocation. Intensivists must therefore be prepared for the next pandemic influenza virus. Preparation requires multiple steps, including careful surveillance for new pandemics, a scalable response system to respond to surge capacity, vaccine production mechanisms, coordinated communication strategies, and stream-lined research plans for timely initiation during a pandemic. Conservative models of a large-scale influenza pandemic predict more than 170% utilization of ICU-level resources. When faced with pandemic influenza, ICUs must have a strategy for resource allocation as strain increases on the system. There are several current threats, including avian influenza A(H5N1) and A(H7N9) viruses. As humans continue to live in closer proximity to each other, travel more extensively, and interact with greater numbers of birds and livestock, the risk of emergence of the next pandemic influenza virus mounts. Now is the time to prepare and coordinate local, national, and global efforts.

scholarly journals A multiplex real-time PCR assay for detection of oseltamivir-resistant strains of influenza virus

2014 ◽  
Vol 9 (6) ◽  
pp. 628-633
Author(s):  
Dawid Nidzworski ◽  
Joanna Dobkowska ◽  
Marcin Hołysz ◽  
Beata Gromadzka ◽  
Bogusław Szewczyk
Keyword(s):  
Real Time ◽  
Influenza A Virus ◽  
Real Time Pcr ◽  
Influenza A ◽  
Influenza Pandemic ◽  
Neuraminidase Inhibitor ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Influenza A Viruses ◽  
Oseltamivir Resistance

AbstractInfluenza is a contagious disease of humans and animals caused by viruses belonging to the Orthomyxoviridae family. The influenza A virus genome consists of negative sense, single-stranded, segmented RNA. Influenza viruses are classified into subtypes based on two surface antigens known as hemagglutinin (H) and neuraminidase (N). The main problem with influenza A viruses infecting humans is drug resistance, which is caused by antigenic changes. A few antiviral drugs are available, but the most popular is the neuraminidase inhibitor — oseltamivir. The resistance against this drug has probably developed through antigenic drift by a point mutation in one amino acid at position 275 (H275Y). In order to prevent a possible influenza pandemic it is necessary to develop fast diagnostic tests. The aim of this project was to develop a new test for detection of influenza A virus and determination of oseltamivir resistance/sensitivity in humans. Detection and differentiation of oseltamivir resistance/sensitivity of influenza A virus was based on real-time PCR. This test contains two TaqMan probes, which work at different wavelengths. Application of techniques like multiplex real-time PCR has greatly enhanced the capability for surveillance and characterization of influenza viruses. After its potential validation, this test can be used for diagnosis before treatment.

scholarly journals Haemagglutinin mutations and glycosylation changes shaped the 2012/13 influenza A(H3N2) epidemic, Houston, Texas

2015 ◽  
Vol 20 (18) ◽  
Author(s):  
K M Stucker ◽  
S A Schobel ◽  
R J Olsen ◽  
H L Hodges ◽  
X Lin ◽  
...  
Keyword(s):  
Vaccine Strain ◽  
Influenza A ◽  
Selection Process ◽  
Influenza Pandemic ◽  
Phylogenetic Analyses ◽  
H1n1 Influenza ◽  
Antigenic Drift ◽  
Antigenic Analysis ◽  
Epidemic Season ◽  
H3n2 Vaccine

While the early start and higher intensity of the 2012/13 influenza A virus (IAV) epidemic was not unprecedented, it was the first IAV epidemic season since the 2009 H1N1 influenza pandemic where the H3N2 subtype predominated. We directly sequenced the genomes of 154 H3N2 clinical specimens collected throughout the epidemic to better understand the evolution of H3N2 strains and to inform the H3N2 vaccine selection process. Phylogenetic analyses indicated that multiple co-circulating clades and continual antigenic drift in the haemagglutinin (HA) of clades 5, 3A, and 3C, with the evolution of a new 3C subgroup (3C-2012/13), were the driving causes of the epidemic. Drift variants contained HA substitutions and alterations in the potential N-linked glycosylation sites of HA. Antigenic analysis demonstrated that viruses in the emerging subclade 3C.3 and subgroup 3C-2012/13 were not well inhibited by antisera generated against the 3C.1 vaccine strains used for the 2012/13 (A/Victoria/361/2011) or 2013/14 (A/Texas/50/2012) seasons. Our data support updating the H3N2 vaccine strain to a clade 3C.2 or 3C.3-like strain or a subclade that has drifted further. They also underscore the challenges in vaccine strain selection, particularly regarding HA and neuraminidase substitutions derived during laboratory passage that may alter antigenic testing accuracy.

scholarly journals The predicted antigenicity of the haemagglutinin of the 1918 Spanish influenza pandemic suggests an avian origin

2001 ◽  
Vol 356 (1416) ◽  
pp. 1871-1876 ◽  
Author(s):  
G. G. Brownlee ◽  
E. Fodor
Keyword(s):  
Influenza A ◽  
Influenza Pandemic ◽  
Consensus Sequence ◽  
Antigenic Drift ◽  
Species Barrier ◽  
Spanish Influenza ◽  
Avian Virus ◽  
Influenza Strain ◽  
Antigenic Sites ◽  
Avian Origin

In 1982 we characterized the antigenic sites of the haemagglutinin of influenza A/PR/8/34, which is an influenza strain of the H1 subtype that was isolated from humans in 1934, by studying mutants which escaped neutralization by antibody. Four antigenic sites, namely Cb, Sa, Sb and Ca, were found to be located near the tip of the trimeric haemagglutinin spike. Based on the sequence of the haemagglutinin of the 1918 Spanish influenza, we can now specify the extent of divergence of antigenic sites of the haemagglutinin during the antigenic drift of the virus between 1918 and 1934. This divergence was much more extensive (40%) than the divergence (20%) in predicted antigenic sites between the 1918 Spanish influenza and an avian H1 subtype consensus sequence. These results support the hypothesis that the human 1918 pandemic originated from an avian virus of the H1 subtype that crossed the species barrier from birds to humans and adapted to humans, presumably by mutation and/or reassortment, shortly before 1918.

scholarly journals Influenza A(H5N1): an overview of the current situation

2009 ◽  
Vol 14 (20) ◽  
Author(s):  
A Melidou ◽  
G Gioula ◽  
M Exindari ◽  
D Chatzidimitriou ◽  
E Diza-Mataftsi
Keyword(s):  
Influenza A ◽  
H5n1 Virus ◽  
H1n1 Virus ◽  
Influenza Pandemic ◽  
Influenza Viruses ◽  
World Health ◽  
Genetic Evolution ◽  
The European Union ◽  
The World ◽  
Health Organization

Influenza viruses continue to threaten the world with a new pandemic. While currently attention is focused on the newly emerged A(H1N1) virus, the avian influenza A(H5N1) virus is still a cause of concern. Extended research is focused on the genetic evolution of the viruses, as well as their susceptibility to available antiviral drugs. One of the major priorities of the World Health Organization is to develop candidate vaccines, four of which are already licensed for use in the European Union. Since the last influenza pandemic in 1968, our knowledge of the influenza virus and its biology has greatly increased, revealing new avenues in the research for antiviral strategies and the development of effective vaccines.

scholarly journals The Molecular Basis for Antigenic Drift of Human A/H2N2 Influenza Viruses

2019 ◽  
Vol 93 (8) ◽  
Author(s):  
M. Linster ◽  
E. J. A. Schrauwen ◽  
S. van der Vliet ◽  
D. F. Burke ◽  
P. Lexmond ◽  
...  
Keyword(s):  
Amino Acid ◽  
Influenza A ◽  
Influenza Pandemic ◽  
Virus Evolution ◽  
Influenza Viruses ◽  
Antigenic Drift ◽  
Amino Acid Substitutions ◽  
Receptor Binding Site ◽  
Antigenic Evolution ◽  
H2n2 Virus

ABSTRACTInfluenza A/H2N2 viruses caused a pandemic in 1957 and continued to circulate in humans until 1968. The antigenic evolution of A/H2N2 viruses over time and the amino acid substitutions responsible for this antigenic evolution are not known. Here, the antigenic diversity of a representative set of human A/H2N2 viruses isolated between 1957 and 1968 was characterized. The antigenic change of influenza A/H2N2 viruses during the 12 years that this virus circulated was modest. Two amino acid substitutions, T128D and N139K, located in the head domain of the H2 hemagglutinin (HA) molecule, were identified as important determinants of antigenic change during A/H2N2 virus evolution. The rate of A/H2N2 virus antigenic evolution during the 12-year period after introduction in humans was half that of A/H3N2 viruses, despite similar rates of genetic change.IMPORTANCEWhile influenza A viruses of subtype H2N2 were at the origin of the Asian influenza pandemic, little is known about the antigenic changes that occurred during the twelve years of circulation in humans, the role of preexisting immunity, and the evolutionary rates of the virus. In this study, the antigenic map derived from hemagglutination inhibition (HI) titers of cell-cultured virus isolates and ferret postinfection sera displayed a directional evolution of viruses away from earlier isolates. Furthermore, individual mutations in close proximity to the receptor-binding site of the HA molecule determined the antigenic reactivity, confirming that individual amino acid substitutions in A/H2N2 viruses can confer major antigenic changes. This study adds to our understanding of virus evolution with respect to antigenic variability, rates of virus evolution, and potential escape mutants of A/H2N2.

scholarly journals Modelling study suggests pandemic influenza could be controlled at source

2005 ◽  
Vol 10 (32) ◽  
Author(s):  
M Cooke ◽  
J Van-Tam
Keyword(s):  
Avian Influenza ◽  
Influenza A ◽  
H5n1 Virus ◽  
Highly Pathogenic Avian Influenza ◽  
Influenza Pandemic ◽  
South East Asia ◽  
Human Influenza ◽  
Highly Pathogenic ◽  
Pathogenic Avian Influenza ◽  
Influenza Outbreaks

The highly pathogenic avian influenza A (H5N1) virus which is causing influenza outbreaks in South East Asia represents the most plausible candidate for a pandemic human influenza strain since the last influenza pandemic in 1968

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