Observations on Influenza Viri Phylogony. 02/04/07 Bioinformatics: Hatem Nassrat

Size: px
Start display at page:

Download "Observations on Influenza Viri Phylogony. 02/04/07 Bioinformatics: Hatem Nassrat"

Transcription

1 Observations on Influenza Viri Phylogony

2 Introduction Influenza Viri Mutation Differences: in sequence structure and protein function between different mutations Likelihood Calculation: to determine the likelihood of a mutation between two different influenza viri proteins

3 Procedure To calculate the likelihood of the mutation, the sequences have to undergo certain computations Influenza Viri protein pairs are generated and searched for within the Influenza database Sequence pairs that have both protein 1 and protein 2, coming from the same strain are placed in Fasta files. Fasta files are aligned using Clustalw The allignments are passed to Phyml for likelihood computation

4 Procedure FLU Find all sequences with protein X, and Y where they appear within the same strain Fasta file seq with X Fasta file seq with Y Fasta File with matching seq concatonated Clustalw Likelihood values For the three computed trees Phyml

5 Input Data Sequences from a group of viri Along with other attributes: Organism from which the strain was sequenced The virus protein found within the sequence A definition of the protein

6 Input Data h_type n_type protein strain definition gi seq H1 N2 PB1 A/duck/NC/91347/01(H1N2) polymerase subunit PB1 [Influenza A virus (A/duck/NC/91347/01(H1N2))] MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/2433/98(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/2433/98(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/604/99(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/604/99(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/790/97(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/790/97(h1n MDVNPTLLF... H1 N2 PB1 A/swine/Cotes d'armor/800/00(h1n2) polymerase subunit 1 [Influenza A virus (A/swine/Cotes d'armor/800/00(h1n TLLFLKVPAQNA... H1 N2 PB1 A/swine/Italy/1081/00(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1081/00(H1N2))] LLFLKVPAQNAI... H1 N2 PB1 A/swine/Italy/1521/98(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1521/98(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Italy/2064/99(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/2064/99(H1N2))] FLKVPAQNAIST.. H1 N2 PB1 A/Swine/Korea/CY02/02(H1N2) polymerase subunit 1 [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/48235/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/48235/04(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/52156/03(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/52156/03(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Ontario/55383/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/55383/04(H1N2)) MDVNPTLLFLK... H1 N2 PB1 A/swine/Scotland/410440/94(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/swine/Zhejiang/1/2004(H1N2) PB1 [Influenza A virus (A/swine/Zhejiang/1/2004(H1N2))] MDVNPTLLFLK... H1 N2 PB1 A/Yokohama/22/2002(H1N2) polymerase subunit 1 [Influenza A virus (A/Yokohama/22/2002(H1N2))] MDVNPTLLFLK...

7 Hunting Sequences The sequences are in a MySQL database To get the sequences SQL similar to the following is used: SELECT A.*,B.* FROM influenza_a A, influenza_a B WHERE A.strain = B.strain AND A.protein = X AND B.protein = Y AND A.h_type = B.h_type and A.n_type = B.n_type AND A.h_type = H_range and A.n_type = N_range A.* area of result belongs to all applicable seq with protein X Similarly B.* represents protein Y The three Fasta files are generated from this result

8 Alignment The contents of the Fasta files are sent to Clustalw for alignment Clustalw options are set to make the output readable by Phyml (PHYLIB)

9 Phyml A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood The aligned sequences are passed to this algorithm Three likelihood values are computed: Likelihood of seq w/ Protein X (L1) Likelihood of seq w/ Protein Y (L2) Likelihood of concat. seqs w/ Protein X.Y (L12)

10 Likelihood This likelihood is used to compute a measure of the probablity of a mutation between viri with protein X to viri with protein Y Mutation Likelihood = L1 + L2 L12 The closer the number is to zero the easier the mutation between the two viri sequences

11 Experiment and Results The Expirement was setup as described earlier A MySQL db with many influenza viri seqs was used to gather the data A program was written to encapsulate the illustrated procedure and combinatorially find the different proteins and ranges to be searched Likelihood values were calculated and compiled

12 Experiment and Results Many total likelihood values where close to zero while others were quite higher Examples with high values include the proteins PA, NP within the H1/N2 range gi h_type n_type protein strain definition seq H1 N2 PA A/swine/Bakum/1832/00(H1N2) polymerase acidic protein [Influenza A virus (A/swine/Bakum/1832/00(H1N2))]. MKEHGEDPK H1 N2 NP A/swine/Bakum/1832/00(H1N2) nucleoprotein [Influenza A virus (A/swine/Bakum/1832/00(H1N2))]. MVMELIRMIK H1 N2 NP A/duck/NC/91347/01(H1N2) nucleoprotein [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MASQGTKRS H1 N2 PA A/duck/NC/91347/01(H1N2) acidic protein 2 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MEDFVRQCFN The total likelihood for these two proteins is

13 Experiment and Results Other Findings Proteins PB1, NA (within H1/N2) (lk = ) Gi h_type n_type protein strain definition Seq H1 N2 NA A/swine/Italy/1081/00(H1N2) neuraminidase [Influenza A virus (A/swine/Italy/1081/00(H1N2))]. IITIGSVS H1 N2 PB1 A/swine/Italy/1081/00(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1081/00(H1N2))]. LLFLKVPA H1 N2 NA A/swine/Italy/1521/98(H1N2) neuraminidase [Influenza A virus (A/swine/Italy/1521/98(H1N2))]. TIGSVSLS H1 N2 PB1 A/swine/Italy/1521/98(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Italy/1521/98(H1N2))]. MDVNPTL H1 N2 PB1 A/Swine/Korea/CY02/02(H1N2) polymerase subunit 1 [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))]. MDVNPTL H1 N2 NA A/Swine/Korea/CY02/02(H1N2) neuraminidase [Influenza A virus (A/Swine/Korea/CY02/02(H1N2))]. MNPNQKI... Proteins PB1, NS2 (within H1/N2) (lk = ) Gi h_type n_type protein strain definition Seq H1 N2 NS2 A/duck/NC/91347/01(H1N2) nonstructural protein 2 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MDSNTVSSFQ H1 N2 PB1 A/duck/NC/91347/01(H1N2) polymerase subunit PB1 [Influenza A virus (A/duck/NC/91347/01(H1N2))]. MDVNPTLLFL H1 N2 PB1 A/duck/NZL/41/1984(H1N2) polymerase PB1 [Influenza A virus (A/duck/NZL/41/1984(H1N2))]. MDVNPTLLFL H1 N2 NS2 A/duck/NZL/41/1984(H1N2) nonstructural protein 2 [Influenza A virus (A/duck/NZL/41/1984(H1N2))]. MDSNTVSSFQ H1 N2 NS2 A/swine/Ontario/55383/04(H1N2) nonstructural protein 2 [Influenza A virus (A/swine/Ontario/55383/04(H1N2))]. MDSNTVSSFQ H1 N2 PB1 A/swine/Ontario/55383/04(H1N2) polymerase subunit PB1 [Influenza A virus (A/swine/Ontario/55383/04(H1N2))]MDVNPTLLFL H1 N2 NS2 A/swine/Scotland/410440/94(H1N2) non structural protein 2 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))MDSNTVSSFQ H1 N2 PB1 A/swine/Scotland/410440/94(H1N2) polymerase subunit 1 [Influenza A virus (A/swine/Scotland/410440/94(H1N2))].MDVNPTLLFL

14 Experiment and Results Proteins PB2, PB1 (within H2/N2) (lk = ) Gi h_type n_type protein strain definition Seq H2 N2 PB2 A/duck/Hong Kong/319/1978(H2N2) polymerase PB2 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MERIKELR H2 N2 PB1 A/duck/Hong Kong/319/1978(H2N2) polymerase PB1 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MDVNPTLL H2 N2 PB2 A/Canada/720/05(H2N2) PB2 polymerase subunit [Influenza A virus (A/Canada/720/05(H2N2))]. MERIKELR H2 N2 PB1 A/Canada/720/05(H2N2) PB1 polymerase subunit [Influenza A virus (A/Canada/720/05(H2N2))]. MDVNPTLL... Proteins PB2, NP (within H2/N2) (lk = ) Gi h_type n_type protein strain definition Seq H2 N2 PB2 A/duck/Hong Kong/319/1978(H2N2) polymerase PB2 [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MERIKELRD H2 N2 NP A/duck/Hong Kong/319/1978(H2N2) nucleocapsid protein [Influenza A virus (A/duck/Hong Kong/319/1978(H2N2))]. MASQGTKRS H2 N2 NP A/Georgia/1/67(H2N2) nucleoprotein [Influenza A virus (A/Georgia/1/67(H2N2))]. MASQGTKR H2 N2 PB2 A/Georgia/1/67(H2N2) PB2 polymerase subunit [Influenza A virus (A/Georgia/1/67(H2N2))]. MERIKE...

15 Conclusions Not many trees had diverse likelihoods as to maximize the total likelihood Many of the sequences with large total likelihoods appeared in ducks and swine Many of the pairs that had a high score tend to have a polymerase unit in the pair

16 Thank You Questions?

Evolutionary distances between proteins of the Influenza A Virus

Evolutionary distances between proteins of the Influenza A Virus Evolutionary distances between proteins of the Influenza A Virus Hatem Nassrat B00393388 Bioinformatics: Winter 06/07 Dr. Christian Blouin Table of Contents Evolutionary distances between proteins of the

More information

Origins and evolutionary genomics of the novel avian-origin H7N9 influenza A virus in China: Early findings

Origins and evolutionary genomics of the novel avian-origin H7N9 influenza A virus in China: Early findings Origins and evolutionary genomics of the novel 2013 avian-origin H7N9 influenza A virus in : Early findings Jiankui He*, Luwen Ning, Yin Tong Department of Biology, South University of Science and Technology

More information

PROTOCOL FOR INFLUENZA A VIRUS GLOBAL SWINE H1 CLADE CLASSIFICATION

PROTOCOL FOR INFLUENZA A VIRUS GLOBAL SWINE H1 CLADE CLASSIFICATION PROTOCOL FOR INFLUENZA A VIRUS GLOBAL SWINE H1 CLADE CLASSIFICATION January 23, 2017 1. Background Swine H1 viruses have diversified into three major genetic lineages over time. Recently, Anderson et al.

More information

Phylogenetic Methods

Phylogenetic Methods Phylogenetic Methods Multiple Sequence lignment Pairwise distance matrix lustering algorithms: NJ, UPM - guide trees Phylogenetic trees Nucleotide vs. amino acid sequences for phylogenies ) Nucleotides:

More information

Study the Evolution of the Avian Influenza Virus

Study the Evolution of the Avian Influenza Virus Designing an Algorithm to Study the Evolution of the Avian Influenza Virus Arti Khana Mentor: Takis Benos Rachel Brower-Sinning Department of Computational Biology University of Pittsburgh Overview Introduction

More information

EVOLUTIONARY TRAJECTORY ANALYSIS: RECENT ENHANCEMENTS. R. Burke Squires

EVOLUTIONARY TRAJECTORY ANALYSIS: RECENT ENHANCEMENTS. R. Burke Squires EVOLUTIONARY TRAJECTORY ANALYSIS: RECENT ENHANCEMENTS R. Burke Squires Pandemic H1N1 2009 Origin? April / May 2009 Cases of an Influenza-like Illness (ILI) occurred in California, Texas and Mexico New

More information

C l u s t e r a n a ly s i s o f t h e o r i g i n s o f t h e n e w i n f l u e n z a A ( H 1 N 1 ) v i r u s

C l u s t e r a n a ly s i s o f t h e o r i g i n s o f t h e n e w i n f l u e n z a A ( H 1 N 1 ) v i r u s R a p i d c o m m u n i c a ti o n s C l u s t e r a n a ly s i s o f t h e o r i g i n s o f t h e n e w i n f l u e n z a A ( H 1 N 1 ) v i r u s A Solovyov 1, G Palacios 2, T Briese 2, W I Lipkin 2,

More information

Influenza Viruses A Review

Influenza Viruses A Review Influenza Viruses A Review AVIAN INFLUENZA: INTERSECTORAL COLLABORATION Larnaca, Cyprus 20 22 July 2009 Kate Glynn Scientific and Technical Department, OIE Influenza Viruses C. Goldsmith,1981 Influenza

More information

Lecture 19 Evolution and human health

Lecture 19 Evolution and human health Lecture 19 Evolution and human health The evolution of flu viruses The evolution of flu viruses Google Flu Trends data US data Check out: http://www.google.org/flutrends/ The evolution of flu viruses the

More information

Pandemic Influenza influenza epidemic: realization of a worst-case scenario

Pandemic Influenza influenza epidemic: realization of a worst-case scenario Pandemic Influenza October 9, 2006 1918 influenza epidemic: realization of a worst-case scenario First case: Albert Mitchell, Camp Funston, KS, March 11, 1918 Up to 20% of all humans infected 20-50 million

More information

I N T R O D U C T I O N

I N T R O D U C T I O N I N T R O D U C T I O N Wednesday 5 April 2017 Jérôme BAUDON, Head of Avian Strategic Business Unit Boehringer Ingelheim THE NEW BOEHRINGER INGELHEIM Merial is now part of the Boehringer Ingelheim family.

More information

http://nmhm.washingtondc.museum/collections/archives/agalleries/1918flu/ncp1603.jpg 1 https://assets-production-webvanta-com.s3-us-west- 2 2.amazonaws.com/000000/47/62/original/images/img_109_influenza/Spanish_flu_death_chart.jpg

More information

In April 2009, a new strain of

In April 2009, a new strain of managing and reducing Uncertainty in an Emerging Influenza Pandemic 2. Brundage JF, Shanks GD. Deaths from bacterial pneumonia during 1918 19 influenza pandemic. Emerg Infect Dis 2008;14:1193-9. 3. Update:

More information

Following virus recombination and evolution

Following virus recombination and evolution Following virus recombination and evolution Coping with the avalanche of sequencing data Dmitry Kusnetsov, Anne Gleizes, Robin Liechti, Ioannis Xenarios, Philippe Le Mercier Vital-IT/Swiss-Prot group SIB

More information

Appendix 81. From OPENFLU to OPENFMD. Open Session of the EuFMD: 2012, Jerez de la Frontera, Spain 1. Conclusions and recommendations

Appendix 81. From OPENFLU to OPENFMD. Open Session of the EuFMD: 2012, Jerez de la Frontera, Spain 1. Conclusions and recommendations From OPENFLU to OPENFMD a resource for automatic and curated nomenclature and tools for the FMD community Filip Claes, Philippe Le Mercier, Dmitry Kuznetsov, Robin Liechti, Anne Gleizes, Ioannis Xenarios,

More information

Nucleic acid Strands Family Example Accession Base pairs

Nucleic acid Strands Family Example Accession Base pairs Table 16.1 Classification of viruses based on nucleic acid composition. Note that NCBI BioProject accessions begin PRJNA and typically encompass several segments. Adapted from Schaechter et al. (1999)

More information

Fondation Merieux J Craig Venter Institute Bioinformatics Workshop. December 5 8, 2017

Fondation Merieux J Craig Venter Institute Bioinformatics Workshop. December 5 8, 2017 Fondation Merieux J Craig Venter Institute Bioinformatics Workshop December 5 8, 2017 Module 5: Comparative Genomics Analysis Outline Definition of comparative genomics Applications in studying human pathogens

More information

SEQUENCE FEATURE VARIANT TYPES

SEQUENCE FEATURE VARIANT TYPES SEQUENCE FEATURE VARIANT TYPES DEFINITION OF SFVT: The Sequence Feature Variant Type (SFVT) component in IRD (http://www.fludb.org) is a relatively novel approach that delineates specific regions, called

More information

Evolution of influenza

Evolution of influenza Evolution of influenza Today: 1. Global health impact of flu - why should we care? 2. - what are the components of the virus and how do they change? 3. Where does influenza come from? - are there animal

More information

Bioinformation Volume 5

Bioinformation Volume 5 Identification of sequence mutations affecting hemagglutinin specificity to sialic acid receptor in influenza A virus subtypes Usman Sumo Friend Tambunan*, Ramdhan Department of Chemistry, Faculty of Mathematics

More information

Relative activity (%) SC35M

Relative activity (%) SC35M a 125 Bat (H17N) b 125 A/WSN (H1N1) Relative activity (%) 0 75 50 25 Relative activity (%) 0 75 50 25 0 Pos. Neg. PA PB1 Pos. Neg. NP PA PB1 PB2 0 Pos. Neg. NP PA PB1 PB2 SC35M Bat Supplementary Figure

More information

Influenza viruses. Virion. Genome. Genes and proteins. Viruses and hosts. Diseases. Distinctive characteristics

Influenza viruses. Virion. Genome. Genes and proteins. Viruses and hosts. Diseases. Distinctive characteristics Influenza viruses Virion Genome Genes and proteins Viruses and hosts Diseases Distinctive characteristics Virion Enveloped particles, quasi-spherical or filamentous Diameter 80-120 nm Envelope is derived

More information

Existence of reassortant A (H1N2) swine influenza viruses in Saitama Prefecture, Japan

Existence of reassortant A (H1N2) swine influenza viruses in Saitama Prefecture, Japan International Congress Series 1263 (2004) 749 753 Existence of reassortant A (H1N2) swine influenza viruses in Saitama Prefecture, Japan Shin ichi Shimada a, *, Takayasu Ohtsuka b, Masayuki Tanaka b, Munehito

More information

Human Influenza. Dr. Sina Soleimani. Human Viral Vaccine Quality Control 89/2/29. November 2, 2011 HVVQC ١

Human Influenza. Dr. Sina Soleimani. Human Viral Vaccine Quality Control 89/2/29. November 2, 2011 HVVQC ١ Human Influenza Dr. Sina Soleimani Human Viral Vaccine Quality Control 89/2/29 November 2, 2011 HVVQC ١ Presentation outline 1. Introduction 2. Virology 3. Classification 4. Hosts 5. Antigenic Specifications

More information

RNA Secondary Structures: A Case Study on Viruses Bioinformatics Senior Project John Acampado Under the guidance of Dr. Jason Wang

RNA Secondary Structures: A Case Study on Viruses Bioinformatics Senior Project John Acampado Under the guidance of Dr. Jason Wang RNA Secondary Structures: A Case Study on Viruses Bioinformatics Senior Project John Acampado Under the guidance of Dr. Jason Wang Table of Contents Overview RSpredict JAVA RSpredict WebServer RNAstructure

More information

Preparing for the Fall Flu Season. Jonathan Gubbay Medical Microbiologist Public Health Laboratory OAHPP

Preparing for the Fall Flu Season. Jonathan Gubbay Medical Microbiologist Public Health Laboratory OAHPP Preparing for the Fall Flu Season Laboratory Perspective Jonathan Gubbay Medical Microbiologist Public Health Laboratory OAHPP September 21, 2009 Objectives 1. Review the emergence of Novel Influenza A

More information

a. From the grey navigation bar, mouse over Analyze & Visualize and click Annotate Nucleotide Sequences.

a. From the grey navigation bar, mouse over Analyze & Visualize and click Annotate Nucleotide Sequences. Section D. Custom sequence annotation After this exercise you should be able to use the annotation pipelines provided by the Influenza Research Database (IRD) and Virus Pathogen Resource (ViPR) to annotate

More information

Student Handout Bioinformatics

Student Handout Bioinformatics Student Handout Bioinformatics Introduction HIV-1 mutates very rapidly. Because of its high mutation rate, the virus will continue to change (evolve) after a person is infected. Thus, within an infected

More information

AutoOrthoGen. Multiple Genome Alignment and Comparison

AutoOrthoGen. Multiple Genome Alignment and Comparison AutoOrthoGen Multiple Genome Alignment and Comparison Orion Buske, Yogesh Saletore, Kris Weber CSE 428 Spring 2009 Martin Tompa Computer Science and Engineering University of Washington, Seattle, WA Abstract

More information

RIT influenza virus database and evidence for differential selection pressures on geographically distinct human influenza A/H3N2 virus populations

RIT influenza virus database and evidence for differential selection pressures on geographically distinct human influenza A/H3N2 virus populations Rochester Institute of Technology RIT Scholar Works Theses Thesis/Dissertation Collections 1-1-2011 RIT influenza virus database and evidence for differential selection pressures on geographically distinct

More information

Introduction to Avian Influenza

Introduction to Avian Influenza Introduction to Avian Influenza David L. Suarez D.V.M., Ph.D. Research Leader Exotic and Emerging Avian Viral Disease Research Unit Agricultural Research Service United States Department of Agriculture

More information

The BLAST search on NCBI ( and GISAID

The BLAST search on NCBI (    and GISAID Supplemental materials and methods The BLAST search on NCBI (http:// www.ncbi.nlm.nih.gov) and GISAID (http://www.platform.gisaid.org) showed that hemagglutinin (HA) gene of North American H5N1, H5N2 and

More information

Project PRACE 1IP, WP7.4

Project PRACE 1IP, WP7.4 Project PRACE 1IP, WP7.4 Plamenka Borovska, Veska Gancheva Computer Systems Department Technical University of Sofia The Team is consists of 5 members: 2 Professors; 1 Assist. Professor; 2 Researchers;

More information

Reassortment of influenza A virus genes linked to PB1 polymerase gene

Reassortment of influenza A virus genes linked to PB1 polymerase gene International Congress Series 1263 (2004) 714 718 Reassortment of influenza A virus genes linked to PB1 polymerase gene Jean C. Downie* www.ics-elsevier.com Centre for Infectious Diseases and Microbiology,

More information

Computational Analysis and Visualization of the Evolution of Influenza Virus

Computational Analysis and Visualization of the Evolution of Influenza Virus Computational Analysis and Visualization of the Evolution of Influenza Virus A DISSERTATION SUBMITTED TO THE FACULTY OF THE GRADUATE SCHOOL OF THE UNIVERSITY OF MINNESOTA BY Ham Ching, Lam IN PARTIAL FULFILLMENT

More information

INFLUENZA VIRUS. INFLUENZA VIRUS CDC WEBSITE

INFLUENZA VIRUS. INFLUENZA VIRUS CDC WEBSITE INFLUENZA VIRUS INFLUENZA VIRUS CDC WEBSITE http://www.cdc.gov/ncidod/diseases/flu/fluinfo.htm 1 THE IMPACT OF INFLUENZA Deaths: PANDEMICS 1918-19 S p a n is h flu 5 0 0,0 0 0 U S 2 0,0 0 0,0 0 0 w o rld

More information

Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2

Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence: NP, PA, PB1, and PB2 Vol.2, No.10, 1138-1147 (2010) http://dx.doi.org/10.4236/ns.2010.210141 Natural Science Correlated mutations in the four influenza proteins essential for viral RNA synthesis, host adaptation, and virulence:

More information

Strategies for control of influenza by targeting broadly conserved viral features

Strategies for control of influenza by targeting broadly conserved viral features Strategies for control of influenza by targeting broadly conserved viral features Forum on Microbial Threats Institute of Medicine June 16, 2004 Suzanne Epstein, Ph.D. Laboratory of Immunology and Developmental

More information

Influenza H3N2 Virus Variation Analysis

Influenza H3N2 Virus Variation Analysis Influenza H3N2 Virus Variation Analysis Objective Upon completion of this exercise, you will be able to: search for virus sequences and view detailed information about these sequences in IRD, build a phylogenetic

More information

Exploring HIV Evolution: An Opportunity for Research Sam Donovan and Anton E. Weisstein

Exploring HIV Evolution: An Opportunity for Research Sam Donovan and Anton E. Weisstein Microbes Count! 137 Video IV: Reading the Code of Life Human Immunodeficiency Virus (HIV), like other retroviruses, has a much higher mutation rate than is typically found in organisms that do not go through

More information

Influenza Prevention Update

Influenza Prevention Update Influenza Prevention Update Dean A. Blumberg, MD, FAAP Disclosure speakers bureau: sanofi pasteur, Merck Discussion off label use of FDA approved vaccines Influenza Prevention Update Seasonal influenza

More information

Università degli Studi di Padova

Università degli Studi di Padova Università degli Studi di Padova Dipartimento di Fisica e Astronomia Galileo Galilei Corso di laurea magistrale in Fisica Statistical inference methods in biophysics Relatore interno: Prof. Amos Maritan

More information

Development of safe and immunogenic reassortant viruses with 5:3 genotype for live attenuated influenza vaccine

Development of safe and immunogenic reassortant viruses with 5:3 genotype for live attenuated influenza vaccine Development of safe and immunogenic reassortant viruses with 5:3 genotype for live attenuated influenza vaccine Irina Isakova-Sivak, PhD Institute of Experimental Medicine, Saint Petersburg, Russia The

More information

Section B. Comparative Genomics Analysis of Influenza H5N2 Viruses. Objective

Section B. Comparative Genomics Analysis of Influenza H5N2 Viruses. Objective Section B. Comparative Genomics Analysis of Influenza H5N2 Viruses Objective Upon completion of this exercise, you will be able to use the Influenza Research Database (IRD; http://www.fludb.org/) to: Search

More information

Modeling the Antigenic Evolution of Influenza Viruses from Sequences

Modeling the Antigenic Evolution of Influenza Viruses from Sequences Modeling the Antigenic Evolution of Influenza Viruses from Sequences Taijiao Jiang Center of Systems Medicine, Chinese Academy of Medical Sciences Suzhou Institute of Systems Medicine October 8-10, 2015.

More information

The Flu: The Virus, The Vaccine, and Surveillance. Joanna Malukiewicz GK12 Program School of Life Sciences Arizona State University

The Flu: The Virus, The Vaccine, and Surveillance. Joanna Malukiewicz GK12 Program School of Life Sciences Arizona State University The Flu: The Virus, The Vaccine, and Surveillance Joanna Malukiewicz GK12 Program School of Life Sciences Arizona State University What do we know about the flu? What kind of bug is it? How do you know

More information

Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza

Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza Ward et al. BMC Evolutionary Biology 2013, 13:222 RESEARCH ARTICLE Open Access Evolutionary interactions between haemagglutinin and neuraminidase in avian influenza Melissa J Ward 1*, Samantha J Lycett

More information

Characterization of the 1918 influenza virus polymerase genes

Characterization of the 1918 influenza virus polymerase genes Vol 437 6 October 2005 doi:10.1038/nature04230 Characterization of the 1918 influenza virus polymerase genes Jeffery K. Taubenberger 1, Ann H. Reid 1, Raina M. Lourens 1, Ruixue Wang 1, Guozhong Jin 1

More information

Introduction to Bioinformatics

Introduction to Bioinformatics Introduction to Bioinformatics Sirkka-Liisa Varvio sirkka-liisa.varvio@helsinki.fi Autumn 2009, I period www.cs.helsinki.fi/mbi/courses/09-10/itb 582606 Introduction to Bioinformatics, Autumn 2009 8. Sept

More information

Pandemic Preparedness

Pandemic Preparedness Pandemic Preparedness Breakfast with the Chiefs October 2, 2009 8:00-9:30 a.m. Please visit our website at www.oahpp.ca What we do: 1. Better information for better public health decisions and actions

More information

Mapping the Antigenic and Genetic Evolution of Influenza Virus

Mapping the Antigenic and Genetic Evolution of Influenza Virus Mapping the Antigenic and Genetic Evolution of Influenza Virus Derek J. Smith, Alan S. Lapedes, Jan C. de Jong, Theo M. Bestebroer, Guus F. Rimmelzwaan, Albert D. M. E. Osterhaus, Ron A. M. Fouchier Science

More information

The "Flu" a case of low fever and sniffles that keeps you home in bed for a day a gastrointestinal upset ("stomach flu")

The Flu a case of low fever and sniffles that keeps you home in bed for a day a gastrointestinal upset (stomach flu) The "Flu" Influenza is a viral infection of the lungs characterized by fever, cough, and severe muscle aches. In the elderly and infirm, it is a major cause of disability and death (often as a result of

More information

INFLUENZA. By :Nader Alaridah MD, PhD

INFLUENZA. By :Nader Alaridah MD, PhD INFLUENZA By :Nader Alaridah MD, PhD General Consideration Acute viral respiratory illnesses are among the most common of human diseases, accounting for one-half or more of all acute illnesses. Influenza

More information

Segments 7 codes for M1 and M2 proteins (Matrix proteins)

Segments 7 codes for M1 and M2 proteins (Matrix proteins) One Flu over the Cuckoo s nest Dr Rachel Jones Department of Virology NPHS Microbiology Cardiff Whistlestop tour through Flu The virus Some history The Novel Virus Recent events The disease The control

More information

Update on Swine Influenza Virus Surveillance in Vietnam

Update on Swine Influenza Virus Surveillance in Vietnam Update on Swine Influenza Virus Surveillance in Vietnam OFFLU SIV Group technical meeting, 3 4 Dec 2015 OIE Headquarters, Paris Tung Nguyen, DAH-Vietnam Swine Influenza surveillance activities in Vietnam

More information

Sebastian Jaenicke. trnascan-se. Improved detection of trna genes in genomic sequences

Sebastian Jaenicke. trnascan-se. Improved detection of trna genes in genomic sequences Sebastian Jaenicke trnascan-se Improved detection of trna genes in genomic sequences trnascan-se Improved detection of trna genes in genomic sequences 1/15 Overview 1. trnas 2. Existing approaches 3. trnascan-se

More information

Supplementary Figure 1 Weight and body temperature of ferrets inoculated with

Supplementary Figure 1 Weight and body temperature of ferrets inoculated with Supplementary Figure 1 Weight and body temperature of ferrets inoculated with A/Anhui/1/2013 (H7N9) influenza virus. (a) Body temperature and (b) weight change of ferrets after intranasal inoculation with

More information

Patricia Fitzgerald-Bocarsly

Patricia Fitzgerald-Bocarsly FLU Patricia Fitzgerald-Bocarsly October 23, 2008 Orthomyxoviruses Orthomyxo virus (ortho = true or correct ) Negative-sense RNA virus (complementary to mrna) Five different genera Influenza A, B, C Thogotovirus

More information

Lecture 18 Evolution and human health

Lecture 18 Evolution and human health Lecture 18 Evolution and human health Evolution and human health 1. Genetic factors 2. Infectious diseases Evolution and human health 1. Genetic factors Evolution and human health 1. Genetic factors P

More information

SWINE FLU 3: NOW NAMED H1N1 INFLUENZA A

SWINE FLU 3: NOW NAMED H1N1 INFLUENZA A 1 Created by LifeWind International SWINE FLU 3: NOW NAMED H1N1 INFLUENZA A Date: 5/09 (1 HOUR) OBJECTIVES: After working through this lesson, participants will be able to: 1. Explain how swine flu spreads

More information

Diagnosis of H1N1 (2009) at the CSIRO Australian Animal Health Laboratory

Diagnosis of H1N1 (2009) at the CSIRO Australian Animal Health Laboratory Diagnosis of H1N1 (2009) at the CSIRO Australian Animal Health Laboratory Peter Daniels and Paul Selleck Prepared for the 2 nd OFFLU Technical Meeting OIE Paris, 15 & 16 September, 2009 AAHL holds the

More information

Seasonal Influenza Report

Seasonal Influenza Report Seasonal Influenza Report 218 219 CDC Disease Week 45 (November 4 November 1, 218) Updated November 13, 218 Key findings for the 218 219 flu season Current Week (Week 45) Current Season Summary November

More information

C th NATIONAL RADIO SCIENCE CONFERENCE (NRSC 2011) April 26 28, 2011, National Telecommunication Institute, Egypt

C th NATIONAL RADIO SCIENCE CONFERENCE (NRSC 2011) April 26 28, 2011, National Telecommunication Institute, Egypt Abstract Genomic signatures and associative classification of the Hemagglutinin protein for Human versus Avian versus Swine Influenza A viruses Fayroz F. Sherif #1, Mahmoud El Hefnawi *2, Yasser Kadah

More information

Multiple sequence alignment

Multiple sequence alignment Multiple sequence alignment Bas. Dutilh Systems Biology: Bioinformatic Data Analysis Utrecht University, February 18 th 2016 Protein alignments We have seen how to create a pairwise alignment of two sequences

More information

Rapid Detection FAQs

Rapid Detection FAQs Rapid Detection FAQs 3M Rapid Detection Reader What are the dimensions of the Rapid Detection Reader? The Rapid Detection Reader includes the Control Module and the Test Module. The Control Module is 185

More information

Targeted disruption of influenza A virus hemagglutinin in genetically modified. mice reduces viral replication and improves disease outcome

Targeted disruption of influenza A virus hemagglutinin in genetically modified. mice reduces viral replication and improves disease outcome Supplementary Information Targeted disruption of influenza A virus hemagglutinin in genetically modified mice reduces viral replication and improves disease outcome Song Wang 1#, Chao Chen 1#, Zhou Yang

More information

Swine Flu, Fiction or Reality

Swine Flu, Fiction or Reality Philadelphia University, Jordan From the SelectedWorks of Philadelphia University, Jordan 2009 Swine Flu, Fiction or Reality Philadelphia University, Philadelphia University Available at: https://works.bepress.com/philadelphia_university/98/

More information

Genetic alterations of histone lysine methyltransferases and their significance in breast cancer

Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Genetic alterations of histone lysine methyltransferases and their significance in breast cancer Supplementary Materials and Methods Phylogenetic tree of the HMT superfamily The phylogeny outlined in the

More information

FREQUENTLY ASKED QUESTIONS 1 Avian Influenza in Birds

FREQUENTLY ASKED QUESTIONS 1 Avian Influenza in Birds FREQUENTLY ASKED QUESTIONS 1 Avian Influenza in Birds What is Avian Influenza? The disease commonly referred to as bird flu is an animal infection caused by the H5N1 virus. The virus occurs naturally among

More information

Treatment of Influenza. Dr. YU Wai Cho

Treatment of Influenza. Dr. YU Wai Cho Treatment of Influenza Dr. YU Wai Cho Symptomatic Treatment Analgesics/ Antipyretics (avoid aspirin) Adequate fluids Rest Specific Drug Treatment Synthetic amines Amantadine Rimantadine Neuraminidase inhibitors

More information

NOVEL H1N1 INFLUENZA EPIDEMIC: Lessons From A Tertiary Centre In Bangalore

NOVEL H1N1 INFLUENZA EPIDEMIC: Lessons From A Tertiary Centre In Bangalore ISPUB.COM The Internet Journal of Pulmonary Medicine Volume 12 Number 1 NOVEL H1N1 INFLUENZA EPIDEMIC: Lessons From A Tertiary Centre In Bangalore B Bhushan, C Nagaraja Citation B Bhushan, C Nagaraja.

More information

2009 (Pandemic) H1N1 Influenza Virus

2009 (Pandemic) H1N1 Influenza Virus 2009 (Pandemic) H1N1 Influenza Virus September 15, 2009 Olympia, Washington Anthony A Marfin Washington State Department of Health Goals Understand current situation & pattern of transmission of 2009 H1N1

More information

Design and implementation of web-based genotyping system of Newcastle disease viruse

Design and implementation of web-based genotyping system of Newcastle disease viruse International Conference on Mechatronics, Control and Electronic Engineering (MCE 2014) Design and implementation of web-based genotyping system of Newcastle disease viruse Yongzhong Cao College of Veterinary

More information

Influenza A H1N1 HA ELISA Pair Set

Influenza A H1N1 HA ELISA Pair Set Influenza A H1N1 HA ELISA Pair Set for H1N1 ( A/Puerto Rico/8/1934 ) HA Catalog Number : SEK11684 To achieve the best assay results, this manual must be read carefully before using this product and the

More information

Lecture 2 Evolution in action: the HIV virus

Lecture 2 Evolution in action: the HIV virus Lecture 2 Evolution in action: the HIV virus Peter and Rosemary Grant Barry Sinervo The HIV/AIDS pandemic Life expectancy in Botswana What is HIV? What is HIV? HIV is a retrovirus (i.e., RNA-based) with

More information

Influenza A H1N1 (Swine Flu 2009) Hemagglutinin / HA ELISA Pair Set

Influenza A H1N1 (Swine Flu 2009) Hemagglutinin / HA ELISA Pair Set Influenza A H1N1 (Swine Flu 2009) Hemagglutinin / HA ELISA Pair Set Catalog Number : SEK001 To achieve the best assay results, this manual must be read carefully before using this product and the assay

More information

Current Vaccines: Progress & Challenges. Influenza Vaccine what are the challenges?

Current Vaccines: Progress & Challenges. Influenza Vaccine what are the challenges? Current Vaccines: Progress & Challenges Influenza Vaccine what are the challenges? Professor John S. Tam The Hong Kong Polytechnic University Asia-Pacific Alliance for the Control of Influenza (APACI)

More information

The Virus. The Respiratory Viruses. Influenza virus. Orthomyxovirus Family

The Virus. The Respiratory Viruses. Influenza virus. Orthomyxovirus Family The Virus The Respiratory Viruses Influenza, RSV, and Rhinoviruses Orthomyxovirus Family Influenza A, B, and C Enveloped viruses with single strand, negative sense RNA genomes RNA is segmented 8 segments

More information

بسم هللا الرحمن الرحيم

بسم هللا الرحمن الرحيم - 1 - - - 1 P a g e بسم هللا الرحمن الرحيم This sheet was made from record section 1 all information are included - Introduction Our respiratory tract is divided anatomically to upper (URT),middle and

More information

Flu, Avian Flu and emerging aspects (H1N1 resistance)

Flu, Avian Flu and emerging aspects (H1N1 resistance) EU-CIS Seminar New trends in Infectious Diseases 26 28 November 2008 / Lyon, France Flu, Avian Flu and emerging aspects (H1N1 resistance) Pr. Florence MORFIN FRE 3011 Université Lyon 1 - CNRS Laboratory

More information

TECHNICAL MEETING 15 April 2015 Athens, Georgia, USA WHO-VCM and new OFFLU- VCM for AI vaccine update

TECHNICAL MEETING 15 April 2015 Athens, Georgia, USA WHO-VCM and new OFFLU- VCM for AI vaccine update TECHNICAL MEETING 15 April 2015 Athens, Georgia, USA WHO-VCM and new OFFLU- VCM for AI vaccine update Vaccines/Vaccination Technical Activity - David E Swayne WHO VCM Work Plan Continued WHO VCM consultation,

More information

Texas Influenza Summary Report, Season (September 28, 2008 April 11, 2009)

Texas Influenza Summary Report, Season (September 28, 2008 April 11, 2009) Texas Influenza Summary Report, 2008 2009 Season (September 28, 2008 April 11, 2009) Background Influenza and influenza-like illnesses (ILI) were last reportable by law in any county in Texas in 1993 (1).

More information

Problem Set 1 September 10, 2009

Problem Set 1 September 10, 2009 September 10, 2009 This problem set consists of three problems designed to reinforce your knowledge of protein structure and energetics and to develop your skills at computationally analyzing protein sequences

More information

Protein Modeling Event

Protein Modeling Event Protein Modeling Event School Name: School Number: Team Member 1: Team Member 2: : Pre-Build Score: On-Site Build Score: Test Score: Tie Breaker: Total: Final Rank: Part I: Pre-Build (40% of total score)

More information

Respiratory Viruses. Respiratory Syncytial Virus

Respiratory Viruses. Respiratory Syncytial Virus Adam Ratner, MD Respiratory Viruses Respiratory viruses are among the most common causes of disease throughout life. Often mild and self-limited, they are still associated with tremendous economic and

More information

The Respiratory Viruses

The Respiratory Viruses The Respiratory Viruses Influenza, RSV, and Rhinoviruses Viruses that gain access to the body through the respiratory tract Some of the most common causes of symptomatic human infections Viral upper respiratory

More information

ph1n1 H3N2: A Novel Influenza Virus Reassortment

ph1n1 H3N2: A Novel Influenza Virus Reassortment ph1n1 H3N2: A Novel Influenza Virus Reassortment Jonathan Gubbay Medical Microbiologist Public Health Laboratory Public Health Ontario June 16, 2011 ph1n1 H3N2 Reassortment: Talk Overview Explain strain

More information

Original Article Development and Sequence Analysis of a Cold-Adapted Strain of Influenza A/New Caledonia/20/1999(H1N1) Virus

Original Article Development and Sequence Analysis of a Cold-Adapted Strain of Influenza A/New Caledonia/20/1999(H1N1) Virus Iranian Journal of Virology 2011;5(4): 6-10 2011, Iranian Society for Virology Original Article Development and Sequence Analysis of a Cold-Adapted Strain of Influenza A/New Caledonia/20/1999(H1N1) Virus

More information

Module 3. Genomic data and annotations in public databases Exercises Custom sequence annotation

Module 3. Genomic data and annotations in public databases Exercises Custom sequence annotation Module 3. Genomic data and annotations in public databases Exercises Custom sequence annotation Objectives Upon completion of this exercise, you will be able to use the annotation pipelines provided by

More information

DOWNLOAD OR READ : SWINE FLU PDF EBOOK EPUB MOBI

DOWNLOAD OR READ : SWINE FLU PDF EBOOK EPUB MOBI DOWNLOAD OR READ : SWINE FLU PDF EBOOK EPUB MOBI Page 1 Page 2 swine flu swine flu pdf swine flu Swine Influenza (swine flu) is a respiratory disease of pigs caused by type A influenza virus that regularly

More information

Envelope e_ :------, Envelope glycoproteins e_ ~ Single-stranded RNA ----, Nucleocapsid

Envelope e_ :------, Envelope glycoproteins e_ ~ Single-stranded RNA ----, Nucleocapsid Virus Antib(tdies Your Expertise, Our Antibodies, Accelerated Discovery. Envelope e_---------:------, Envelope glycoproteins e_-------1~ Single-stranded RNA ----, Nucleocapsid First identified in 1989,

More information

Nermin Ashraf Shaltout

Nermin Ashraf Shaltout THE AMERICAN UNIVERSITY IN CAIRO SCHOOL OF SCIENCES AND ENGINEERING Improving Machine Learning Techniques for Influenza-A Classification A THESIS DEFENSE SUBMITTED TO DEPARTMENT OF COMPUTER SCIENCE AND

More information

Understanding Flu Testing

Understanding Flu Testing TECHNICAL BULLETIN Vol. 1 No. 2, August 2005 Understanding Flu Testing 1 Flu Facts 2 Choosing a Rapid Flu A+B Test 4 Improved Medical Outcomes 5 Enhanced Economic Value 8 9 BD Directigen EZ Flu A+B Technology:

More information

Influenza Surveillance United States and Global

Influenza Surveillance United States and Global Influenza Surveillance 2008-09 United States and Global Raymond A. Strikas, MD National Vaccine Program Office Department of Health and Human Services With grateful thanks to Lyn Finelli, DrPH, and Anthony

More information

Flu Vaccination. John Hann, MD UC Irvine Health

Flu Vaccination. John Hann, MD UC Irvine Health Flu Vaccination John Hann, MD UC Irvine Health So you got the flu. What to do about. Influenza spread in US https://www.cdc.gov/flu/weekly/ Influenza spread world wide http://apps.who.int/flumart/default?reportno=6

More information

Molecular epidemiology of Newcastle disease and avian influenza in South Africa

Molecular epidemiology of Newcastle disease and avian influenza in South Africa Molecular epidemiology of Newcastle disease and avian influenza in South Africa by C. ABOLNIK Submitted in partial fulfillment of the requirements for the degree Philosophiae Doctor in the Faculty of Natural

More information

Laboratory Diagnosis of Viral Infections affect the Lower Respiratory Tract. M Parsania, Ph.D. Tehran Medical Branch, Islamic Azad University

Laboratory Diagnosis of Viral Infections affect the Lower Respiratory Tract. M Parsania, Ph.D. Tehran Medical Branch, Islamic Azad University Laboratory Diagnosis of Viral Infections affect the Lower Respiratory Tract M Parsania, Ph.D. Tehran Medical Branch, Islamic Azad University Overview of viral infections affect the lower respiratory tract

More information

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza

Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza Host Dependent Evolutionary Patterns and the Origin of 2009 H1N1 Pandemic Influenza The origin of H1N1pdm constitutes an unresolved mystery, as its most recently observed ancestors were isolated in pigs

More information

A Bioinformatics Approach to Analyzing Influenza Ray Hylock

A Bioinformatics Approach to Analyzing Influenza Ray Hylock A Bioinformatics Approach to Analyzing Influenza Ray Hylock 1 Introduction During its annual emergence, influenza causes 3 to 5 million severe illness cases and 250 to 500 thousand deaths. Receiving a

More information

Cristina Cassetti, Ph.D.

Cristina Cassetti, Ph.D. NIAID Extramural Research Update: Recombinant Influenza Viruses and Biosafety Cristina Cassetti, Ph.D. Influenza Program Officer Division of Microbiology and Infectious Diseases NIAID Influenza virus DMID

More information