Figure 1. Phylogenetic tree of H5N1 viruses sequenced in this study, in addition to other publicly available H5Nx clade 2.3.4.4 from GenBank and GISAID. Red dots represent the H5N1 viruses sequenced in this study. Topological support values (SH-like support) of selected nodes are displayed. To the right, a schematic representation of viral clustering of each gene segment (from left to right: PB2, PB1, polymerase acidic, haemagglutinin, nucleoprotein, neuraminidase, matrix, and non-structural) is shown. Segment colors indicate origin of the segment. Within each cluster, a unified color pattern indicates homogeneity and a different color pattern indicates reassortment.

Figure 1. Phylogenetic tree of H5N1 viruses sequenced in this study, in addition to other publicly available H5Nx clade 2.3.4.4 from GenBank and GISAID. Red dots represent the H5N1 viruses sequenced in this study. Topological support values (SH-like support) of selected nodes are displayed. To the right, a schematic representation of viral clustering of each gene segment (from left to right: PB2, PB1, polymerase acidic, haemagglutinin, nucleoprotein, neuraminidase, matrix, and non-structural) is shown. Segment colors indicate origin of the segment. Within each cluster, a unified color pattern indicates homogeneity and a different color pattern indicates reassortment.

Figure 2. Time to the most recent common ancestor of H5N1 viruses sequenced in this study; maximum clade credibility temporal phylogeny of the hemagglutinin (HA) gene. The H5N1 viruses from Egypt are represented by red dots. Posterior clade probabilities are indicated by the sizes of the internal node circles. Shaded bars represent the 95% highest probability distribution for the age of each node with posterior clade probability > 0.3.

Table 1. Comparison of nucleotide sequence identities of the eight influenza A virus (IAV) gene sequences for the virus isolated in this study (A/pintail/Egypt/RA19853OP/2021 (H5N1)) and nearest virus homologs.

Table 1. Comparison of nucleotide sequence identities of the eight influenza A virus (IAV) gene sequences for the virus isolated in this study (A/pintail/Egypt/RA19853OP/2021 (H5N1)) and nearest virus homologs.

Gene *Accession No.VirusCollection Date% IdentityPB2EPI2082687A/Great white pelican/Israel/123/2022 (A/H5N1)2022-01-1299 EPI1922962 †A/duck/Saratov/29-08V/2021 (H5N1)2021-09-30 99PB1EPI2085772A/common kestel/Israel/49-2/2022 (A/H5N1)2022-01-0299.63 EPI1922971A/duck/Saratov/29-11V/2021 (A/H5N1)2021-09-3099.96PAEPI207623A/chicken/Israel/88/2022 (A/H5N1)2022-01-09 99 EPI1922969A/duck/Saratov/29-11V/2021 (A/H5N1)2021-09-3099HAEPI_ISL_418175A/European herring gull/Sweden/SVA211116SZ0432/FB004518/M-2021 (A/H5N1)2021-11-08 99NPEPI2085770A/common kestel/Israel/49-2/2022 (A/H5N1)2022-01-0299 EPI1922966A/duck/Saratov/29-11V/2021 (A/H5N1)2021-09-30 99NAEPI2085768A/common kestel/Israel/49-2/2022 (A/H5N1)2022-01-02 99 EPI1963383A/guineafowl/Scotland/054471/2021 (A/H5N1) 2021-11-01 99MEPI2085769A/common kestel/Israel/49-2/2022 (A/H5N1)2022-01-02100 EPI1922960A/duck/Saratov/29-08V/2021 (A/H5N1)2021-09-30100NSEPI2008127A/black-headed_gull/England/388256/2022 (A/H5N1)2022-02-0399 EPI1938848A/barnacle goose/Sweden/SVA211111SZ0376/FB004496/2021 (A/H5N1)2021-11-01 99

Table 2. Assessment of molecular amino acid markers for zoonotic potential of the influenza A(H5N1) virus detected in Egypt.

Table 2. Assessment of molecular amino acid markers for zoonotic potential of the influenza A(H5N1) virus detected in Egypt.

Viral
ProteinAmino AcidA/Pintail/Egypt/RA19853OP/2021 (H5N1)Functional RelevanceReferencesPB2E627KEMammalian host adaptation[24]D701NDIncrease polymerase activity and viral replication in mammalian cells[25]L89VVEnhanced polymerase activity, increased virulence in mice[26]G309DDT339KKA588VAMammalian host adaptation[27]PB1-F2N66SSIncreases virulence, replication efficiency, and the antiviral response in mammals[28,29]PAV100AVContributed to the virulence and mammalian adaptation[30]S409NSA515TTIncreased polymerase activity, increased virulence in mammals and birds[31]HAE198DEEnhanced mammalian receptor binding[32]Q234LQPreferential binding to human Sialic acid α2–6 receptor[33,34]G236SGI155TTEnhanced mammalian receptor binding[35]NAE119VEOseltamivir resistance[36,37]H275YHR293KRN295SNM2L26PLReduced susceptibility to amantadine[38,39,40]V27A/IVA30TAS31NSG34EGNS1P42SSIncreased virulence and pathogenicity in mammals[41,42,43]D92EDV149AA

Table 3. Antigenic analysis of H5N1 influenza A viruses from Egypt by hemagglutination inhibition assay.

Table 3. Antigenic analysis of H5N1 influenza A viruses from Egypt by hemagglutination inhibition assay.

F.2015-7 *F.2017-13F.2016-16F.2015-48 A/duck/England/36254/2014A/chicken/Kumamoto/1-7/14A/Gyrfalcon/WA/41088/2014A/Sichuan/26221/2014A/duck/England/36254/2014320256012802560A/chicken/Kumamoto/1-7/144080<40<40A/Gyrfalcon/WA/41088/2014160640320320A/Sichuan/26221/20148080<4080A/Pintail/Egypt/RA19853OP/202132064064040A/duck/Egypt/BA20360C/2022 160640320160A/duck/Egypt/BA20361C/2022 640128012801280A/duck/Egypt/BA20361OP/2022 160640320160