Computational protocol: Immunity toward H1N1 influenza hemagglutinin of historical and contemporary strains suggests protection and vaccine failure

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Protocol publication

[…] Phylogenetic analysis of influenza hemagglutinin DNA sequences were conducted in MEGA5 using the Maximum Likelihood method based on the Tamura-Nei model, 500 bootstrap repetitions were performed. To analyze the protein similarity of influenza hemagglutinin from different H1N1 strains, the aminoacid sequences from the protein region HA135-295 were aligned using ClustalW2. This region of the HA protein is part of the hemagglutinin receptor binding domain (HA-RBD), which is located in the external surface of the virus and it concentrates most of the antigenic potential of the HA protein. Amino Acid HA GenBank accession numbers for Clustal alignment (): A/NewCaledonia/20/1999(H1N1) (AAP34324.1); A/SolomonIslands/3/2006(H1N1) (ABU99109.1); A/Brisbane/59/2007(H1N1) (ADE28750.1). Amino Acid HA GenBank accession numbers for homology table (): A/BrevigMission/1/1918 (AAD17218); A/PuertoRico/8/1934 (CAA24272); A/AA/Marton/1943-(ABO38054); A/FortMonmouth/1/1947 (ABD77807); A/USSR/90/1977 (ABD95350); A/Taiwan/1/1986 (ABF21274); A/NewCaledonia/20/1999 (ABF21272); A/SolomonIslands/3/2006 (ABU99109); A/Brisbane/59/2007 (ACA28844); California/07/2009 (ACP41953); A/NewYork/18/2009 (ACR67196). GenBank accession numbers for the phylogenetic analysis of HA DNA sequence (): A/PR/8/1934 (V01088); A/BrevigMission/1/1918 (AF116575); A/South Carolina/1/1918 (AF117241); A/AA/Marton/1943 (CY02028); A/FortMonmouth/1/1947 (CY009612); A/USSR/90/1977 (CY010372); A/Taiwan/01/1986 (DQ508873); A/NewCaledonia/20/1999 (DQ508857); A/SolomonIslands/3/2006 (EU124177); A/Brisbane/59/2007 (CY030230); A/California/07/2009 (FJ966974); A/NewYork/18/2009 (GQ232064). […]

Pipeline specifications

Software tools MEGA, Clustal W
Application Phylogenetics
Organisms Mustela putorius furo
Diseases Influenza, Human