Tweet
Citation: Emerging Microbes & Infections (2016) 5, e22; doi:10.1038/emi.2016.48
Published online 16 March 2016
Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic
OPEN
Zheng Zhu1,*, Jasper Fuk-Woo Chan1,2,3,4,*, Kah-Meng Tee1, Garnet Kwan-Yue Choi3, Susanna Kar-Pui Lau1,2,3,4, Patrick Chiu-Yat Woo1,2,3,4, Herman Tse1,2,3,4 and Kwok-Yung Yuen1,2,3,4
*These authors contributed equally to this work.
Received 2 March 2016; Accepted 3 March 2016
Topof page ABSTRACT
Less than 20 sporadic cases of human Zika virus (ZIKV) infection were reported in Africa and Asia before 2007, but large outbreaks involving up to 73% of the populations on the Pacific islands have started since 2007, and spread to the Americas in 2014. Moreover, the clinical manifestation of ZIKV infection has apparently changed, as evident by increasing reports of neurological complications, such as Guillain?Barr? syndrome in adults and congenital anomalies in neonates. We comprehensively compared the genome sequences of pre-epidemic and epidemic ZIKV strains with complete genome or complete polyprotein sequences available in GenBank. Besides the reported phylogenetic clustering of the epidemic strains with the Asian lineage, we found that the topology of phylogenetic tree of all coding regions is the same except that of the non-structural 2B (NS2B) coding region. This finding was confirmed by bootscan analysis and multiple sequence alignment, which suggested the presence of a fragment of genetic recombination at NS2B with that of Spondweni virus. Moreover, the representative epidemic strain possesses one large bulge of nine bases instead of an external loop on the first stem-loop structure at the 3′-untranslated region just distal to the stop codon of the NS5 in the 1947 pre-epidemic prototype strain. Fifteen amino acid substitutions are found in the epidemic strains when compared with the pre-epidemic strains. As mutations in other flaviviruses can be associated with changes in virulence, replication efficiency, antigenic epitopes and host tropism, further studies would be important to ascertain the biological significance of these genomic changes.
hat tip CIDRAP for the link
Published online 16 March 2016
Comparative genomic analysis of pre-epidemic and epidemic Zika virus strains for virological factors potentially associated with the rapidly expanding epidemic
OPEN
Zheng Zhu1,*, Jasper Fuk-Woo Chan1,2,3,4,*, Kah-Meng Tee1, Garnet Kwan-Yue Choi3, Susanna Kar-Pui Lau1,2,3,4, Patrick Chiu-Yat Woo1,2,3,4, Herman Tse1,2,3,4 and Kwok-Yung Yuen1,2,3,4
- 1Department of Microbiology, The University of Hong Kong, Hong Kong, China
- 2State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong, China
- 3Research Centre of Infection and Immunology, The University of Hong Kong, Hong Kong, China
- 4Carol Yu Centre for Infection, The University of Hong Kong, Hong Kong, China
*These authors contributed equally to this work.
Received 2 March 2016; Accepted 3 March 2016
Topof page ABSTRACT
Less than 20 sporadic cases of human Zika virus (ZIKV) infection were reported in Africa and Asia before 2007, but large outbreaks involving up to 73% of the populations on the Pacific islands have started since 2007, and spread to the Americas in 2014. Moreover, the clinical manifestation of ZIKV infection has apparently changed, as evident by increasing reports of neurological complications, such as Guillain?Barr? syndrome in adults and congenital anomalies in neonates. We comprehensively compared the genome sequences of pre-epidemic and epidemic ZIKV strains with complete genome or complete polyprotein sequences available in GenBank. Besides the reported phylogenetic clustering of the epidemic strains with the Asian lineage, we found that the topology of phylogenetic tree of all coding regions is the same except that of the non-structural 2B (NS2B) coding region. This finding was confirmed by bootscan analysis and multiple sequence alignment, which suggested the presence of a fragment of genetic recombination at NS2B with that of Spondweni virus. Moreover, the representative epidemic strain possesses one large bulge of nine bases instead of an external loop on the first stem-loop structure at the 3′-untranslated region just distal to the stop codon of the NS5 in the 1947 pre-epidemic prototype strain. Fifteen amino acid substitutions are found in the epidemic strains when compared with the pre-epidemic strains. As mutations in other flaviviruses can be associated with changes in virulence, replication efficiency, antigenic epitopes and host tropism, further studies would be important to ascertain the biological significance of these genomic changes.
hat tip CIDRAP for the link