Extensive evolution analysis of the global chikungunya virus strains revealed the origination of CHIKV epidemics in Pakistan in 2016
- 148 Downloads
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 lineage-specific 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.
Keywordschikungunya virus (CHIKV) Pakistan phylogenetic analysis
This work was supported by the Science and Technology Basic Work Program (2013FY113500) from the Ministry of Science and Technology of China, the International Cooperation on key Technologies of Biosafety along the China-Pakistan Economic Corridor (153B42KYSB2017 0004), the Strategic Bio-resource Service Network Plan and Building the Biogenetic Resource Preserving Capacity Program from the Chinese Academy of Sciences (ZSSB-002), and was funded by the National Basic Scientific Data Sharing-Service Platform (XXH12504-3-15).
SJ, NJ contributed the human serum sample collection; ZYS and SQL were responsible for obtaining the seven whole genomic sequence of CHIKV; ZJF and JW downloaded the sequences and constructed the datasets; JMS and SS performed the bioinformatic analysis and wrote the primary manuscript; FD, BZ and HPW checked and finalized the manuscript.
Compliance with Ethics Guidelines
The authors declare that they have no conflict of interest. The whole study was approved by the ethics committee of the Wuhan Institute of Virology (WIV), Chinese Academy of Sciences (CAS), China. Written consents were obtained from all the patients involved in the study.
- Abraham R, Manakkadan A, Mudaliar P, Joseph I, Sivakumar KC, Nair RR, Sreekumar E. 2016. Correlation of phylogenetic clade diversification and in vitro infectivity differences among Cos-mopolitan genotype strains of Chikungunya virus. Infect Genet Evol, 37: 174–184.CrossRefPubMedCentralGoogle Scholar
- Afzal MF, Naqvi SQ, Sultan MA, Hanif A. 2015. Chikungunya fever among children presenting with nonspecific febrile illness during an epidemic of dengue fever in Lahore, Pakistan. Merit Res J Med Scis, 3: 69–73.Google Scholar
- Arankalle VA, Shrivastava S, Cherian S, Cherian S, Gunjikar RS, Walimbe AM, Jadhav SM, Sudeep AB, Mishra AC. 2007. Genetic divergence of Chikungunya viruses in India (1963–2006) with special reference to the 2005–2006 explosive epidemic. J Gen Virol, 88: 1967–1976.CrossRefPubMedCentralGoogle Scholar
- Centers for Disease Control and Prevention (CDC). 2006. Chikungunya fever diagnosed among international travelers–United States, 2005–2006. MMWR Morb Mortal Wkly Rep, 55: 1040–1042.Google Scholar
- Delisle E, Rousseau C, Broche B, Leparc-Goffart I, L’Ambert G, Cochet A, Prat C, Foulongne V, Ferre JB, Catelinois O, Flusin O, Tchernonog E, Moussion IE, Wiegandt A, Septfons A, Mendy A, Moyano MB, Laporte L, Maurel J, Jourdain F, Reynes J, Paty MC, Golliot F. 2015. Chikungunya outbreak in Montpellier, France, September to October 2014. Euro Surveill, 20. pii: 21108.CrossRefGoogle Scholar
- Chikungunya virus emergence is constrained in Asia by lineagespecific adaptive landscapes. Kumar S, Nei M, Dudley J, Tamura K. 2008. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform, 9: 299–306.Google Scholar
- Laras K, Sukri NC, Larasati RP, Bangs MJ, Kosim R, Djauzi, Wandra T, Master J, Kosasih H, Hartati S, Beckett C, Sedyaningsih ER, Beecham HJ, 3rd, Corwin AL. 2005. Tracking the re-emergence of epidemic chikungunya virus in Indonesia. Trans R Soc Trop Med Hyg, 99: 128–141.CrossRefPubMedCentralGoogle Scholar
- Liu SQ, Li X, Zhang YN, Gao AL, Deng CL, Li JH, Jehan S, Jamil N, Deng F, Wei HP, Zhang B. 2017. Detection, isolation and characterization of chikungunya virus associated with chikungunya outbreak in Pakistan in 2016-17. Virol Sin, 32. (In Press)Google Scholar
- Rezza G, Nicoletti L, Angelini R, Romi R, Finarelli AC, Panning M, Cordioli P, Fortuna C, Boros S, Magurano F, Silvi G, Angelini P, Dottori M, Ciufolini MG, Majori GC, Cassone A, group Cs. 2007. Infection with chikungunya virus in Italy: an outbreak in a temperate region. Lancet, 370: 1840–1846.CrossRefGoogle Scholar
- Tsetsarkin KA, Chen R, Yun R, Rossi SL, Plante KS, Guerbois M, Forrester N, Perng GC, Sreekumar E, Leal G, Huang J, Mukhopadhyay S, Weaver SC. 2014. Multi-peaked adaptive landscape for chikungunya virus evolution predicts continued fitness optimization in Aedes albopictus mosquitoes. Nat Commun, 5: 4084.CrossRefPubMedCentralGoogle Scholar
- Vanlandingham DL, Hong C, Klingler K, Tsetsarkin K, McElroy KL, McElroy KL, Powers AM, Lehane MJ, Higgs S. 2005. Differential infectivities of o’nyong-nyong and chikungunya virus isolates in Anopheles gambiae and Aedes aegypti mosquitoes. Am J Trop Med Hyg, 72: 616–621.CrossRefPubMedCentralGoogle Scholar
- Volk SM, Chen R, Tsetsarkin KA, Adams AP, Garcia TI, Sall AA, Nasar F, Schuh AJ, Holmes EC, Higgs S, Maharaj PD, Brault AC, Weaver SC. 2010. Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. J Virol, 84: 6497–6504.CrossRefPubMedCentralGoogle Scholar