Zika virus genome from the Americas

On Oct 1, 2015, a 52-year-old man was hospitalised with exanthema and conjunctivitis at the Academic Hospital in Paramaribo, Suriname. During the next few days, four patients were admitted with mild symptoms including exanthema. Sera from these patients were negative for dengue and chikungunya viruses but positive for Zika virus (ZIKV) by specific real-time reverse transcription PCR.1

ZIKV is an emerging arthropodborne virus of the family Flaviviridae. It is transmitted by aedes mosquitoes, as are dengue and chikungunya viruses. First isolated in April, 1947, in Uganda, it was until recently considered to cause sporadic benign human infections in Africa and Asia. After the first documented outbreak on Yap Island, Micronesia, in 2007, however, ZIKV caused a large epidemic in French Polynesia in 2013–14, before spreading throughout the Pacific.2 This large epidemic occurred concomitantly with circulation of dengue viruses and unusual increases in severe neurological complications, such as Guillain-Barré syndrome3 and congenital neurological malformations. Also during 2013–14, chikungunya emerged and spread in the Americas. Soon after, the first evidence was found of the emergence of ZIKV in the Americas, in northeast Brazil in May, 2015.4 Autochthonous circulation of ZIKV in other countries started on Oct 16, 2015, in Colombia, followed by Suriname on Nov 12, 2015.

The first five autochthonous cases detected in Suriname were confirmed by the French National Reference Centre for arboviruses, located at the Pasteur Institute in French Guiana. Viral sequencing was done directly from the sera of four of these viraemic patients. Complete coding of the ZIKV sequence was obtained for one patient and envelope protein coding sequences for the three others.

Few complete genomes are available for ZIKV and, until this analysis, none for ZIKV circulating in the Americas. Phylogenetic analyses were conducted for the NS5 protein coding region, the envelope protein coding region, and the complete coding region, against the sequences available in databases: all the phylogenetic trees showed the same topology. The Suriname strains belong to the Asian genotype and seem to be most closely related to the strain that was circulating in French Polynesia in 2013, with which they share more than 99·7% and 99·9% of nucleotide and aminoacid identity, respectively (figure).

The situation is evolving rapidly, with more countries in South and Central America reporting cases.5 This rapid spread of ZIKV strains closely related to the French Polynesian strains, raises increasing concern for public health. Furthermore, the increased frequency of Guillain-Barré syndrome and congenital neurological anomalies notified by the Brazil Ministry of Health6 should provide impetus for collaborative research programmes to evaluate the relations between ZIKV and these autoimmune and neurological conditions.

We declare no competing interests. Antoine Enfi ssi, John Codrington, Jimmy Roosblad, Mirdad Kazanji,

Figure: Phylogenetic relations between the envelope gene sequences of Suriname ZIKV and other ZIKV Maximum likelihood phylogenetic tree was inferred for sequences from envelope genes of Zika viruses with the GTR+G+I model with four Suriname ZIKV strains (GenBank accession numbers: KU312312 to KU312315, complete genome sequence was obtained for KU312312) and 14 reference ZIKV sequences from GenBank (eight references from the African lineage [accession numbers: KF268948, KF268950, KF268949, LC002520, AY632535, DQ859059, HQ234500, HQ234501] and six references from the Asian lineage [accession numbers: KJ776791, KJ634273, KF993678, JN860885, EU545988, HQ234499]). The contig sequences, obtained from de-novo assembly of Suriname strain sequences and multiple sequence alignments were done with CLC Main Workbench 6.9 Beta 4 software (CLC bio, Aarhus, Denmark). Bootstrap values are indicated at nodes. Scale is shown at the bottom as substitutions per site. ZIKV=Zika virus

*Dominique Rousset drousset@pasteur-cayenne.fr Institut Pasteur de la Guyane, Laboratoire de Virologie, Cayenne, French Guiana, France (AE, MK, DR); and Laboratory Academisch Ziekenhuis, Paramaribo, Suriname (JC, JR)

1 Lanciotti RS, Kosoy OL, Laven JJ, et al. Genetic and serologic properties of Zika virus associated with an epidemic, Yap State, Micronesia, 2007. Emerg Infect Dis 2008; 14: 1232–39.

2 Cao-Lormeau VM, Musso D. Emerging arboviruses in the Pacifi c. Lancet 2014; 384: 1571–72.

3 Oehler E, Watrin L, Larre P, et al. Zika virus infection complicated by Guillain-Barre syndrome–case report, French Polynesia, December 2013. Euro Surveill 2014; 19: pii 20720.

4 Zanluca C, de Melo VC, Mosimann AL, Dos Santos GI, Dos Santos CN, Luz K. First report of autochthonous transmission of Zika virus in Brazil. Mem Inst Oswaldo Cruz 2015; 110: 569–72.

5 WHO. Zika virus outbreaks in the Americas. Wkly Epidemiol Rec 2015; 90: 609–10.

6 ECDC. Zika virus epidemic in the Americas: potential association with microcephaly and Guillain-Barré syndrome. http://ecdc.europa. eu/en/publications/Publications/zika-virusamericas-association-with-microcephaly-rapidrisk-assessment.pdf (accessed Dec 31, 2015).