Characterization and mutational analysis of haemagglutinin and neuraminidase of H3N2 and H1N1pdm09 human influenza A viruses in Egypt

Abstract

Seasonal influenza viruses constitute a major global concern. Currently, H3N2 and H1N1pdm09 are the commonly circulating influenza A viruses. The haemagglutin and neuraminidase genes of influenza A(H3N2) and A(H1N1)pdm09 viruses from Egyptian paediatric patients with respiratory distress were sequenced. Mutational analysis of all published sequences from Egypt was evolutionary tracked for both HA and NA genes. Phylogenetic analysis of H3N2 HA showed that the Egyptian strains belong to 3C2 subclade while Egyptian A(H1N1)pdm09 strains belong to 6B1 subclade. Some Egyptian A(H1N1)pdm09, 2013-2014, strains form a new subclade; 6B3. High score of mutations were recorded in HA of H1N1pdm09 but higher was recorded in H3N2 strains. These findings confirmed a high mutation rate of influenza A subtypes specially H3N2 strains.

Molecular Epidemiology and Evolutionary Dynamics of Human Influenza Type-A Viruses in Africa: A Systematic Review

“…Kenya strains sampled during the 2015–2016 season retained four (11, 23, 87, and 287) of the six classical N-linked glycosylation sites. While all 2015–2017 and 2017–2018 sH1N1pdm09 strains sampled in Egypt [ 101 ] and Kenya [ 61 ], respectively, gained a new N-linked glycosylation site (S162N) present in the A/Michigan/45/2015(H1N1) strain H1 protein, except for one A/Kenya/066/2018(H1N1) strain.…”

“…H1N1pdm09 strains with antigenic site Ca 2 substitution, D222G, associated with disease severity [ 106 ], circulated at lower frequencies in Tunisia (8%, 4/50) and Egypt (9%, 1/17) during the 2009–2011 and 2009 season, respectively [ 49 , 50 , 101 ]. Another D222G variant was sampled in Egypt later in 2016 [ 101 ].…”

“…H1N1pdm09 strains with antigenic site Ca 2 substitution, D222G, associated with disease severity [ 106 ], circulated at lower frequencies in Tunisia (8%, 4/50) and Egypt (9%, 1/17) during the 2009–2011 and 2009 season, respectively [ 49 , 50 , 101 ]. Another D222G variant was sampled in Egypt later in 2016 [ 101 ]. Several HA1 substitutions, S185T, Q293H, K374E, 312I, H138Q, S203T, R205K, D222E, and T288N, were also sporadically observed among patients with severe acute respiratory illnesses (SARI) [ 49 , 50 , 51 , 66 ].…”

“…Several HA1 substitutions, S185T, Q293H, K374E, 312I, H138Q, S203T, R205K, D222E, and T288N, were also sporadically observed among patients with severe acute respiratory illnesses (SARI) [ 49 , 50 , 51 , 66 ]. The D222E variants widely circulated in Tunisia, South Africa, Morocco, Senegal, and Egypt during the pandemic [ 48 , 49 , 50 , 51 , 52 , 66 , 101 ].…”

“…All Africa H1N1pdm09 virus strains sampled between 2009 and 2016 had the M2 adamantane-resistant marker, S31N [ 47 , 54 , 55 , 58 , 105 ], but lacked the N1 oseltamivir-resistance marker, H275Y [ 47 , 48 , 51 , 54 , 55 , 58 , 62 , 63 , 66 , 90 , 101 , 104 ]. Except for a strain sampled from a South African patient after treatment with a standard dose of oseltamivir during the pandemic [ 43 ] and an A/Egypt/1424/2016(H1N1) strain had H275Y in their N1 proteins.…”