Chikungunya virus is Aedes mosquitoe transmitted virus that has typical signs and symptoms of high fever, headache, hemorrhage and body rashes. Although in the past decade millions of people in several continents like Asia, Africa and some islands of Indian Ocean have faced the major outbreaks of Chikungunya virus because of its travel associated febrile nature. An inexplicable paralyzing disease has trapped thousands of people in Karachi region of Pakistan and the symptomatology among suspected cases was compatible with Chikungunya fever. Thus Chikungunya outbreak was reported in Pakistan but actually the recent reports about the occurrence of Chikungunya outbreak in the southern region of Pakistan has been highly controversial. In order to further confirm the circulation of the virus and put an end to the speculative claims for the corresponding outbreak in Pakistan, a study was conducted at the Center of Excellence in Molecular Biology in Lahore. The study included 500 suspected serum samples. All clinical specimens were tested for IgM and IgG specific antibodies against Chikungunya virus using a commercial ELISA kit. Twenty seven (5.4%) and thirty five (7%) samples were IgM and IgG positive, respectively. All antibody positive samples and a subset of negative samples (195) were further subjected to PCR for confirmatory purposes. Two different sets of primers were used for the identification of the viral genome. Thirty samples were found PCR positive and a subset of ten samples was direct sequenced. Sequence analysis showed 94% similarity to Stenotrophomonas maltophilia which is considered to be the second most prevalent bacterial species in mosquitoe’s midgut. This observation may lead towards the confusion that the outbreak is either of Dengue or Chikunguna virus. In conclusion, confirmatory molecular characterization of the viral genome remains controversial and further studies are needed in this respect.
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