title: Molecular diagnosis and phylogenetic analysis of human papillomavirus type-16 from suspected patients in Pakistan.
abstract: BACKGROUND
  Human Papillomavirus (HPV) is well known pathogen that can cause benign and malignant tumors in humans, yet there is very little information regarding HPV types prevalent in Pakistan.
  
  
  METHODS
  A total of 92 cervical secretions were collected from suspected married female patients and used for DNA isolation using a novel isolation method. The samples were tested through Polymerase Chain Reaction (PCR) using already reported primers MY09/MY11, GP5/GP6, GP5+/GP6+, CP65/CP70, CP66/CP69 and SPF1/SPF2 and with those developed in this study including HRT1 and HRT2 primer sets for typing HPV types and HACTB primer set for human beta actin gene as internal positive control. Sequencing and phylogenetic analyses were performed for two isolates to determine circulating HPV types.
  
  
  RESULTS
  PCR with HRT1 and HRT2 indicated 2 (2.17 %) patients were positive for HPV type- 16 while 1 (1.08 %) with HPV type 18. Sequencing and phylogenetic analysis of isolates confirmed HPV type-16 in genus alpha 9 which have 99 % homology with already reported HPV from Japan and Costa Rica.
  
  
  CONCLUSIONS
  This is the first report of HPV type-16 genus alpha 9 in Pakistan and the reported assay and sequence data will serve as valuable tools in further epidemiological studies for HPV surveillance to improve public health, especially of females in Pakistan.
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, 45550 Islamabad, Pakistan ; Department of Biochemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan ; Department of Integrative Engineering, Chung Ang University, Seoul, South Korea.
authors.forename: Abdullah
authors.initials: A
authors.lastname: Abdullah
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, 45550 Islamabad, Pakistan ; Department of Biochemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan ; Immune Network Pioneer Research Centre, School of Medicine, Ajou University, Suwon, South Korea.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Qasim
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, 45550 Islamabad, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Shafiq
authors.affiliation: Department of Clinical Medicine and Surgery, University of Veterinary and Animal Sciences-Lahore, Lahore, Pakistan.
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ijaz
authors.affiliation: Department of Obstetrics and Gynecology, Benazir Bhutto Hospital Rawalpindi, Rawalpindi, Pakistan.
authors.forename: Shamsa
authors.initials: S
authors.lastname: Parveen
authors.affiliation: Department of Clinical Diagnostics, Nuclear Oncology and Radiotherapy Institute, Islamabad, Pakistan.
authors.forename: Shahnaz
authors.initials: S
authors.lastname: Murtaza
authors.affiliation: Department of Biochemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.
authors.forename: Qamar
authors.initials: Q
authors.lastname: Javed
authors.affiliation: Department of Biochemistry, Quaid-i-Azam University Islamabad, Islamabad, Pakistan.
authors.forename: Salman Akbar
authors.initials: SA
authors.lastname: Malik
authors.affiliation: Department of Obstetrics and Gynecology, Nawaz Sharif Medical College, University of Gujrat, Gujrat, Pakistan.
authors.forename: Shahida Husain
authors.initials: SH
authors.lastname: Tarar
authors.affiliation: Department of Biochemistry and Molecular Biology, Nawaz Sharif Medical College, University of Gujrat, Gujrat, Pakistan.
authors.forename: Sajid
authors.initials: S
authors.lastname: Mehmood
authors.affiliation: Department of Biochemistry, PMAS Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan.
authors.forename: Abdul
authors.initials: A
authors.lastname: Sami
authors.affiliation: Department of Biochemistry, PMAS Arid Agriculture University Rawalpindi, Rawalpindi, Pakistan.
authors.forename: Syed Muhammad Saqlan
authors.initials: SM
authors.lastname: Naqvi
authors.affiliation: Department of Biosciences, COMSATS Institute of Information Technology, 45550 Islamabad, Pakistan.
authors.forename: Muhammad Zeeshan
authors.initials: MZ
authors.lastname: Hyder
keywords: Cervical carcinoma; Molecular epidemiology; Papillomavirus; Phylogenetic; Sexually Transmitted Diseases