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Outbreaks involving the Asian genotype Chikungunya virus (CHIKV) caused over one million infections in the Americas recently. The outbreak was preceded by a major nationwide outbreak in the Philippines. We examined the phylogenetic and phylogeographic relationships of representative CHIKV isolates obtained from the 2012 Philippines outbreak with other CHIKV isolates collected globally. Asian CHIKV isolated from the Philippines, China, Micronesia and Caribbean regions were found closely related, herein denoted as Cosmopolitan Asian CHIKV (CACV). Three adaptive amino acid substitutions in nsP3 (D483N), E1 (P397L) and E3 (Q19R) were identified among CACV. Acquisition of the nsP3-483N mutation in Compostela Valley followed by E1-397L/E3-19R in Laguna preceded the nationwide spread in the Philippines. The China isolates possessed two of the amino acid substitutions, nsP3-D483N and E1-P397L whereas the Micronesian and Caribbean CHIKV inherited all the three amino acid substitutions. The unique amino acid substitutions observed among the isolates suggest multiple independent virus dissemination events. The possible biological importance of the specific genetic signatures associated with the rapid global of the virus is not known and warrant future in-depth study and epidemiological follow-up. Molecular evidence, however, supports the Philippines outbreak as the possible origin of the CACV.
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... During the same period, CHIKV E1A226V infected approximately 1.3 million people in India [213,[216][217][218][219][220][221][222][223][224]. The CHIKV E1A226V variant has also been disseminated in Europe, including in Italy (2007) and France [210,225], as well as Papua New Guinea (2012) [226]. Later in December 2013, a major CHIKV epidemic occurred in the Caribbean islands [227][228][229] and, subsequently, there were 22,796 confirmed cases out of approximately 1 million suspected cases reported in 2014 in the Americas [226,230]. ...
... Two sublineages, the Indian Ocean lineage (IOL) and Asian/American, emerged from the ECSA and Asian lineages, respectively [231]. According to distinct geographical territories and temporal factors, the CHIKV Asian lineage is divided into two clades: the Indian and the Southeast Asian (SEA) clades [225]. Differences in the CHIKV genetic properties among lineages and sublineages have caused differences in epidemiology, pathology, and virulence among CHIKV strains [202,231]. ...
... The ECSA lineage and IOL A226V substitution sublineage were responsible for outbreaks in 2005 and onwards, such as those in Réunion Island [211,232], Asia, the Indian Ocean islands, and Europe [211,217,233,234]. Meanwhile, the Asian/American sublineage was the major cause of several epidemics in the Pacific Islands and the Americas [225,235]. ...
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