Influenza sequence and epitope database

Abstract

Influenza epidemics arise through the acquisition of viral genetic changes to overcome immunity from previous infections. An increasing number of complete genomes of influenza viruses have been sequenced in Asia in recent years. Knowledge about the genomes of the seasonal influenza viruses from different countries in Asia is valuable for monitoring and understanding of the emergence, migration and evolution of strains. In order to make full use of the wealth of information from such data, we have developed an integrated user friendly relational database, Influenza Sequence and Epitope Database (ISED), that catalogs the influenza sequence and epitope information obtained in Asia. ISED currently hosts a total of 13 020 influenza A and 2984 influenza B virus sequence data collected in 17 countries including 9 Asian countries, and a total of approximately 545 amantadine-resistant influenza virus sequences collected in Korea. ISED provides users with prebuilt application tools to analyze sequence alignment and different patterns and allows users to visualize epitope-matching structures, which is freely accessible at http://influenza.korea.ac.kr and http://influenza.cdc.go.kr.

Impact of influenza virus escape‐mutations on influenza detection by the rapid influenza diagnostic test

“…The strains of A(H1N1)pdm09 with escape-mutations, which were identified by searching the influenza sequence databases [Bao et al, 2008;Yang et al, 2009], and the wild isolates (which also exhibited escape-mutations) available to us were analyzed using mAbs I38 and D383 and the SDpdm RIDT. The viral isolates A/Sendai/TU406/ 2009 and A/Sendai/TU416/2009, which contain the HA G56E substitution, showed significantly reduced reactivity with mAb I38 and in the HA-based test line of the SDpdm RIDT, but showed no reduction in affinity for mAb D383 (Table I and Fig.…”

“…Non-redundant and complete HA sequences from 1,974 A(H1N1)pdm09 strains (collected between March 2009 and June 2011 in 68 countries) were extracted from the Influenza Virus Resource and the Korea Influenza Sequence and Epitope Database [Bao et al, 2008;Yang et al, 2009] and analyzed. Twelve strains (12/1,974) were found to encode an aa other than glycine at position 56 in HA: G56E, G56R, and G56W substitutions occurred in seven strains, four strains and one strain, respectively (Supplementary Table S1).…”

“…In addition, both the mAbs used in the RIDT and the escape-variants were immunologically characterized. Furthermore, the frequency of the escape-variants (which are predicted to be poorly detected by the RIDT) since the appearance of the pandemic virus was determined by analyzing A(H1N1)pdm09 HA sequences retrieved from influenza sequence databases [Bao et al, 2008;Yang et al, 2009]. Although the frequency determined using the influenza sequence databases does not exactly equal the true frequency of the escape-variants, the data may be beneficial for forecasting and judging whether the RIDT should again be used for the optimal detection of current or future A(H1N1)pdm09 strains.…”

“…RT-PCR and subsequent sequencing of the viral HA, NA, and M segments were performed as previously described [Yi et al, 2010]. The sequences were then analyzed using influenza sequence databases as previously described [Bao et al, 2008;Yang et al, 2009]. HA amino acid (aa) numbering throughout the text starts from the signal peptide of the HA coding region.…”

Computational analysis in Influenza virus

“…IRD is distinctive in the size and intensity of the data and analysis tools provided and in its approach to data and workflow integration that aid in the development of vaccines, therapeutics, and diagnostics [3] . A number of influenza-focused web-accessible databases exist: the NCBI Influenza Virus Resource (IVR) [8] , Global Initiative on Sharing Avian Influenza Data (GISAID) EpiFlu Database [9] , Korea Influenza Sequence & Epitope Database (KISED) [10] , the Influenza Virus Database (IVDB) [11] , and the OpenFlu Database [12] .…”