1. State Key Laboratory of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
2. Centre of Excellence in Science and Applied Technology, Islamabad 44000, Pakistan
Chikungunya virus (CHIKV) is a mosquito-borne virus that causes epidemics widely in the world
especially in the tropical and subtropical regions. Phylogenetic analysis has found that the CHIKV
lineages were associated with the spatial and temporal distributions, which were related to the
virus adaption to the major mosquito species and their distributions. In this study, we reported the
complete genome sequences of eight CHIKV isolates from the outbreak in Pakistan last year. Then
we reviewed the evolutionary history using extensive phylogenetic analysis, analyzed lineagespecific substitutions in viral proteins, and characterized the spreading pathway of CHIKV strains
including the Pakistani strains. The results showed that the Pakistani stains belonged to the
ECSA.IOL sub-lineage and derived from India. The genetic properties of the Pakistani strains
including the adaptive substitution to vectors were further characterized, and the potential risks
from the occurrence of CHIKV infection in Pakistan were discussed. These results provided better
understanding of CHIKV evolution and transmission in the world and revealed the possible
origination of the CHIKV outbreak and epidemic in Pakistan, which would promote the disease
prevention and control in the identified countries and territories with the history of CHIKV
infections as well as new regions with potential risk of CHIKV outbreaks.