title: CCHF virus variants in Pakistan and Afghanistan: Emerging diversity and epidemiology.
abstract: BACKGROUND
  Crimean Congo hemorrhagic fever (CCHF) has been reported from more than 30 countries in Africa, Asia, Eastern Europe and Middle East. The disease is considered endemic in Pakistan and neighboring countries like Iran and Afghanistan.
  
  
  OBJECTIVE
  This study aimed to explore the genetic diversity of CCHF virus (CCHFV) detected in Pakistan and Afghanistan based on analysis of partial S-segment sequences.
  
  
  METHODS
  During 2011, one hundred samples satisfying the CCHF case definition were tested by (ELISA) and RT-PCR for detection of IgM antibodies and viral RNA, respectively. Phylogenetic analysis was carried out on partial S-segment nucleotide sequences using MEGA 5.0.
  
  
  RESULTS
  Out of one hundred collected during 2011, 49 (49%) were positive for CCHF either by ELISA/RT-PCR or both. The mean age of the CCHFV positive cases was 30.32 years (range 18-56 years) and overall mortality rate was 20.4%. All CCHF virus isolates from this study clustered with strains previously reported from Pakistan, Iran and Afghanistan within the Asia-1 genogroup. Four distinct sub-clades were found circulating within Asia-1 genogroup. Six CCHFV strains found in Pakistan and Afghanistan grouped into a new sub-clade-D.
  
  
  CONCLUSIONS
  Data from this study shows that endemic foci of CCHFV span the international border between Pakistan and Afghanistan with genetically diverse variants circulating in this region. Our findings emphasize to establish a laboratory based surveillance program and devise health policy measures to control CCHF infection especially in Baluchistan.
authors.affiliation: Department of Biochemistry, Hazara University, Mansehra, Pakistan.
authors.forename: Adnan
authors.initials: A
authors.lastname: Khurshid
authors.affiliation: Department of Biochemistry, Hazara University, Mansehra, Pakistan.
authors.forename: Mukhtiar
authors.initials: M
authors.lastname: Hassan
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Muhammad Masroor
authors.initials: MM
authors.lastname: Alam
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Uzma Bashir
authors.initials: UB
authors.lastname: Aamir
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Lubna
authors.initials: L
authors.lastname: Rehman
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Salmaan
authors.initials: S
authors.lastname: Sharif
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Shahzad
authors.initials: S
authors.lastname: Shaukat
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Muhammad Suleman
authors.initials: MS
authors.lastname: Rana
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan.
authors.forename: Mehar
authors.initials: M
authors.lastname: Angez
authors.affiliation: Department of Virology, National Institute of Health, Islamabad, Pakistan. Electronic address: sohailz@live.com.
authors.forename: Syed Sohail Zahoor
authors.initials: SS
authors.lastname: Zaidi
mesh_terms: D000293:Adolescent; D000328:Adult; D000346:Afghanistan / Q000453:epidemiology; D000914:Antibodies, Viral / Q000097:blood; D016000:Cluster Analysis; D019353:Endemic Diseases; D004797:Enzyme-Linked Immunosorbent Assay; D005260:Female; D014644:Genetic Variation; D003225:Hemorrhagic Fever Virus, Crimean-Congo / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification*; D006479:Hemorrhagic Fever, Crimean / Q000453:epidemiology* / Q000821:virology*; D006801:Humans; D007075:Immunoglobulin M / Q000097:blood; D008297:Male; D008875:Middle Aged; D017720:Molecular Epidemiology; D010154:Pakistan / Q000453:epidemiology; D010802:Phylogeny; D012367:RNA, Viral / Q000097:blood / Q000235:genetics; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D017385:Sequence Homology; D055815:Young Adult
chemical_list: D000914:Antibodies, Viral; D007075:Immunoglobulin M; D012367:RNA, Viral
keywords: Asia-1 genogroup; CCHF; Genetic diversity; Molecular epidemiology; Pakistan