title: Genomic Surveillance Elucidates Persistent Wild Poliovirus Transmission During 2013-2015 in Major Reservoir Areas of Pakistan.
abstract: BACKGROUND
  Despite tremendous efforts in the fight against polio, Pakistan bears the highest proportion of poliomyelitis cases among the 3 endemic countries including Afghanistan and Nigeria. Apart from insecurity and inaccessibility challenges, the substantial shift of unimmunized children from North Waziristan due to recent military operations was presumed to favor the widespread poliovirus infection in Pakistan.
  
  
  METHODS
  To better understand the current epidemiological situation, we analyzed the virologic data of wild poliovirus type 1 (WPV1) strains detected in Pakistan during 2013-2015.
  
  
  RESULTS
  Five genetic clusters (A-E) were identified with at least 5% nucleotide divergence in the viral protein 1 (VP1) coding region. Peshawar, Quetta, and Karachi were found to be the major endemic foci where multiple discrete genetic lineages of WPV1 were detected. Phylogenetic analysis suggests that wild poliovirus strains from endemic regions were genetically distant (with 5%-15% VP1 nucleotide divergence) from those detected in North Waziristan cases, excluding the possibility of a recent progenitor of WPV1 instigating single-source transmission across the country. Orphan lineages detected in Rawalpindi, Lahore, Hyderabad, Sukkur, and Jacobabad revealed silent transmission and the need for vigilant surveillance. Sustenance of analogous genetic lineages over a period of 3 years highlights multiple unimmunized foci present to maintain viral genetic diversity.
  
  
  CONCLUSIONS
  Our findings are inconsistent with the hypothesis that impoverished populations from North Waziristan serve as a possible determinant of widespread poliomyelitis infection in Pakistan and further emphasize the need to scale-up clinical and environmental surveillance as well as immunization activities.
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Muhammad Masroor
authors.initials: MM
authors.lastname: Alam
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Salmaan
authors.initials: S
authors.lastname: Sharif
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Shahzad
authors.initials: S
authors.lastname: Shaukat
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Mehar
authors.initials: M
authors.lastname: Angez
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Adnan
authors.initials: A
authors.lastname: Khurshid
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Lubna
authors.initials: L
authors.lastname: Rehman
authors.affiliation: Department of Virology, National Institute of Health, Chak Shahzad, Islamabad, Pakistan.
authors.forename: Syed Sohail Zahoor
authors.initials: SSZ
authors.lastname: Zaidi
mesh_terms: D002675:Child, Preschool; D018562:Disease Transmission, Infectious; D062665:Epidemiological Monitoring; D005260:Female; D005838:Genotype; D006801:Humans; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D017720:Molecular Epidemiology; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D011051:Poliomyelitis / Q000453:epidemiology* / Q000635:transmission / Q000821:virology*; D017955:Poliovirus / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification
keywords: North Waziristan; Pakistan; epidemiology; genetic diversity; poliovirus