Comprehensive Genome Scale Phylogenetic Study Provides New Insights on the Global Expansion of Chikungunya Virus

Abstract

Since the India and Indian Ocean outbreaks of 2005 and 2006, the global distribution of chikungunya virus (CHIKV) and the locations of epidemics have dramatically shifted. First, the Indian Ocean lineage (IOL) caused sustained epidemics in India and has radiated to many other countries. Second, the Asian lineage has caused frequent outbreaks in the Pacific islands and in 2013 was introduced into the Caribbean, followed by rapid spread to nearly all of the neotropics. Further, CHIKV epidemics, as well as exported cases, have been reported in central Africa after a long period of perceived silence. To understand these changes and to anticipate the future of the virus, the exact distribution, genetic diversity, transmission routes, and future epidemic potential of CHIKV require further assessment. To do so, we conducted the most comprehensive phylogenetic analysis to date, examined CHIKV evolution and transmission, and explored distinct genetic factors associated with the emergence of the East/Central/ South African (ECSA) lineage, the IOL, and the Asian lineage. Our results reveal contrasting evolutionary patterns among the lineages, with growing genetic diversities observed in each, and suggest that CHIKV will continue to be a major public health threat with the potential for further emergence and spread. IMPORTANCE Chikungunya fever is a reemerging infectious disease that is transmitted by

Development and evaluation of one‐step multiplex real‐time RT‐PCR assay for simultaneous detection of Zika virus and Chikungunya virus

“…Our newly developed detection system displayed the same results as before(Table 4).4 | DISCUSSIONZIKV and CHIKV, following the resembling transmission pathway and sharing the same mosquitoes vectors,6 are displaying a growth trend of endemic and epidemic transmission globally 11,13,14,[27][28][29]. The amounts of viruses in reaction are 10 5 , 10 4 , 10 3 , 10 2 , 10, 1, 0.5, and 0.1 PFU.…”

“…6,7 The two mosquitoborne viruses were firstly discovered in Africa more than 60 years ago. 11,12 Growing human populations, urbanization, climatic changes, international travelling, and trades contribute to the extensive spread of ZIKV and CHIKV to the areas where mosquitoes Aedes have been infested. 11,12 Growing human populations, urbanization, climatic changes, international travelling, and trades contribute to the extensive spread of ZIKV and CHIKV to the areas where mosquitoes Aedes have been infested.…”

“…This one-step multiplex RT-PCR can be used as differential diagnosis in areas where multiple flaviviruses are co-circulating.The phylogenetics of ZIKV and CHIKV were characterized by the divergent evolutionary lineages distributing in different geographic regions 7,8,11,39. The sensitivity of this multiplex assay was demonstrated to be adequate in detection of infectious viruses, with limit of detection up to 1 and 0.5 PFU for ZIKV and CHIKV, respectively.…”

Emerging arboviruses: Why today?

“…The lineage that finally reached St Martin in the Caribbean in 2013 originated from the clade comprising viruses from Indonesia, the South Pacific islands and the Philippines. Significantly, these Asian lineage strains which reached the Americas, did not possess the E1-A226V mutation which enhances transmissibility of CHIKV in Ae albopictus but they retained the E1-A98T amino acid substitution which suppresses the activity of the E1-A226V substitution thus restricting the American lineage viruses to Ae aegypti [76] . …”

“…Eight years later an Asian lineage emerged and rapidly dispersed across islands in the Pacific Ocean reaching St Martin in late 2013 [16], [17], [18]. Following its arrival in the Caribbean, epidemic chikungunya fever with associated long-term arthralgic sequelae, dispersed throughout tropical Latin America.…”