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KHAN, MOHAMMAD ASİF

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MOHAMMAD ASİF
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Author: Abd Raman, Hadia Syahirah ×

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    PublicationOpen Access
    Avian Influenza H7N9 Virus Adaptation to Human Hosts
    (2021-05-01T00:00:00Z) Tan, Swan; Sjaugi, Muhammad Farhan; Fong, Siew Chinn; Chong, Li Chuin; Abd Raman, Hadia Syahirah; Nik Mohamed, Nik Elena; August, Joseph Thomas; Khan, Asif M.; KHAN, MOHAMMAD ASİF
    Avian influenza virus A (H7N9), after circulating in avian hosts for decades, was identified as a human pathogen in 2013. Herein, amino acid substitutions possibly essential for human adaptation were identified by comparing the 4706 aligned overlapping nonamer position sequences (1-9, 2-10, etc.) of the reported 2014 and 2017 avian and human H7N9 datasets. The initial set of virus sequences (as of year 2014) exhibited a total of 109 avian-to-human (A2H) signature amino acid substitutions. Each represented the most prevalent substitution at a given avian virus nonamer position that was selectively adapted as the corresponding index (most prevalent sequence) of the human viruses. The majority of these avian substitutions were long-standing in the evolution of H7N9, and only 17 were first detected in 2013 as possibly essential for the initial human adaptation. Strikingly, continued evolution of the avian H7N9 virus has resulted in avian and human protein sequences that are almost identical. This rapid and continued adaptation of the avian H7N9 virus to the human host, with near identity of the avian and human viruses, is associated with increased human infection and a predicted greater risk of human-to-human transmission.
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    PublicationOpen Access
    Dynamics of Influenza A (H5N1) virus protein sequence diversity
    (2020-05-01T00:00:00Z) Abd Raman, Hadia Syahirah; Tan, Swan; August, Joseph Thomas; Khan, Asif M.; KHAN, MOHAMMAD ASİF
    Background. InfluenzaA(H5N1) virus is a global concern with potential as a pandemic threat. High sequence variability of influenza A viruses is a major challenge for effective vaccine design. A continuing goal towards this is a greater understanding of influenza A (H5N1) proteome sequence diversity in the context of the immune system (antigenic diversity), the dynamics of mutation, and effective strategies to overcome the diversity for vaccine design.
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    g-FLUA2H: a web-based application to study the dynamics of animal-to-human mutation transmission for influenza viruses
    (2015-01-01T00:00:00Z) Sjaugi, Muhammad Farhan; Tan, Swan; Abd Raman, Hadia Syahirah; Lim, Wan Ching; Mohamed, Nik Elena Nik; August, J. Thomas; Khan, Asif M.; KHAN, MOHAMMAD ASİF
    g-FLUA2H is a web-based application focused on the analysis of the dynamics of influenza virus animal-to-human (A2H) mutation transmissions. The application only requires the viral protein sequences from both the animal and human host populations as input datasets. The comparative analyses between the co-aligned sequences of the two viral populations is based on a sliding window approach of size nine for statistical significance and data application to the major histocompatibility complex (MHC) and T-cell receptor (TCR) immune response mechanisms. The sequences at each of the aligned overlapping nonamer positions for the respective virus hosts are classified as four patterns of characteristic diversity motifs, as a basis for quantitative analyses: (i) -index-, the most prevalent sequence; (ii) -major- variant, the second most common sequence and the single most prevalent variant of the index, with at least one amino acid mutation; (iii) -minor- variants, multiple different sequences, each with an incidence (percent occurrence) less than that of the major variant; and (iv) -unique- variants, each with only one occurrence in the alignment. The diversity motifs and their incidences at each of the nonamer positions allow evaluation of the mutation transmission dynamics and selectivity of the viral sequences in relation to the animal and the human hosts. g-FLUA2H is facilitated by a grid back-end for parallel processing of large sequence datasets. The web-application is publicly available at http://bioinfo.perdanauniversity.edu.my/g-FLUA2H. It can be used for a detailed characterization of the composition and incidence of mutations present in the proteomes of influenza viruses from animal and human host populations, for a better understanding of host tropism.