Comparative genome analysis between Southeast Asian and South American Zika viruses

Theerarat Kochakarn; Namfon Kotanan; Krittikorn Kümpornsin; Duangkamon Loesbanluechai; Monta Thammasatta; Prasert Auewarakul; Prapon Wilairat; Thanat Chookajorn

doi:10.1016/j.apjtm.2016.10.002

Comparative genome analysis between Southeast Asian and South American Zika viruses

Asian Pac J Trop Med. 2016 Nov;9(11):1048-1054. doi: 10.1016/j.apjtm.2016.10.002. Epub 2016 Oct 21.

Authors

Theerarat Kochakarn¹, Namfon Kotanan², Krittikorn Kümpornsin², Duangkamon Loesbanluechai³, Monta Thammasatta⁴, Prasert Auewarakul⁵, Prapon Wilairat⁶, Thanat Chookajorn⁷

Affiliations

¹ Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand; Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
² Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand.
³ Department of Clinical Microscopy, Faculty of Allied Health Sciences, Chulalongkorn University Bangkok, Thailand.
⁴ National Science and Technology Development Agency, Pathum Thani, Thailand.
⁵ Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand.
⁶ Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand.
⁷ Genomics and Evolutionary Medicine Unit, Centre of Excellence in Malaria, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. Electronic address: thanat.cho@mahidol.edu.

PMID: 27890363
DOI: 10.1016/j.apjtm.2016.10.002

Abstract

Objective: To understand the cause for the differences between potentially mild Southeast Asian and the more pathogenic ZIKV in South America.

Methods: A comparative genomic analysis was performed to determine putative causations stemming from ZIKV.

Results: Phylogenetic analyses integrating geographical and time factors revealed that Southeast Asian ZIKV might not be the direct source of South American outbreaks as previously speculated. Amino acid residues unique to South American ZIKV isolates at the envelope, pr and NS1 proteins are listed and shown in the structural context. These unique residues on external viral proteins are not found in Southeast Asian ZIKV and could be responsible for the ongoing outbreak either via an intrinsic property of the virus or interactions with human immunity. Only a selected few primer/probe sets currently in clinical use were identified of being capable of detecting ZIKV strains worldwide. The envelope proteins of dengue virus (DENV) and ZIKV also showed a remarkable degree of similarity especially at the surface residues.

Conclusions: These findings may help explain the cross-reactivity of DENV antibodies to ZIKV. Thus, major caveats must be exercised in using existing diagnostic tools for ZIKV.

Keywords: Dengue virus; Phylogenetic analysis; Protein structure; Southeast Asia; Zika virus.