title: Phylogeography of influenza A H5N1 clade 2.2.1.1 in Egypt.
abstract: BACKGROUND
  Influenza A H5N1 has killed millions of birds and raises serious public health concern because of its potential to spread to humans and cause a global pandemic. While the early focus was in Asia, recent evidence suggests that Egypt is a new epicenter for the disease. This includes characterization of a variant clade 2.2.1.1, which has been found almost exclusively in Egypt.We analyzed 226 HA and 92 NA sequences with an emphasis on the H5N1 2.2.1.1 strains in Egypt using a Bayesian discrete phylogeography approach. This allowed modeling of virus dispersion between Egyptian governorates including the most likely origin.
  
  
  RESULTS
  Phylogeography models of hemagglutinin (HA) and neuraminidase (NA) suggest Ash Sharqiyah as the origin of virus spread, however the support is weak based on Kullback-Leibler values of 0.09 for HA and 0.01 for NA. Association Index (AI) values and Parsimony Scores (PS) were significant (p-value < 0.05), indicating that dispersion of H5N1 in Egypt was geographically structured. In addition, the Ash Sharqiyah to Al Gharbiyah and Al Fayyum to Al Qalyubiyah routes had the strongest statistical support.
  
  
  CONCLUSIONS
  We found that the majority of routes with strong statistical support were in the heavily populated Delta region. In particular, the Al Qalyubiyah governorate appears to represent a popular location for virus transition as it represented a large portion of branches in both trees. However, there remains uncertainty about virus dispersion to and from this location and thus more research needs to be conducted in order to examine this.Phylogeography can highlight the drivers of H5N1 emergence and spread. This knowledge can be used to target public health efforts to reduce morbidity and mortality. For Egypt, future work should focus on using data about vaccination and live bird markets in phylogeography models to study their impact on H5N1 diffusion within the country.
authors: Department of Biomedical Informatics, Arizona State University, 13212 E Shea Blvd, Samuel C Johnson Bldg, Scottsdale, AZ 85259, USA. matthew.scotch@asu.edu.
authors: Matthew
authors: M
authors: Scotch
authors: Changjiang
authors: C
authors: Mei
authors: Yilma J
authors: YJ
authors: Makonnen
authors: Julio
authors: J
authors: Pinto
authors: AbdelHakim
authors: A
authors: Ali
authors: Sally
authors: S
authors: Vegso
authors: Michael
authors: M
authors: Kane
authors: Indra Neil
authors: IN
authors: Sarkar
authors: Peter
authors: P
authors: Rabinowitz
mesh_terms: D000818:Animals; D001499:Bayes Theorem; D001717:Birds / Q000821:virology; D004534:Egypt / Q000453:epidemiology; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification / Q000235:genetics*; D005585:Influenza in Birds / Q000453:epidemiology*; D008390:Markov Chains; D008957:Models, Genetic; D009010:Monte Carlo Method; D009439:Neuraminidase / Q000235:genetics; D058974:Phylogeography
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; D009439:Neuraminidase