Zika virus in the Americas: early epidemiological and genetic findings
Faria NR., Azevedo RS., Kraemer MU., Souza R., Cunha MS., Hill SC., Thézé J., Bonsall MB., Bowden TA., Rissanen I., Rocco IM., Nogueira JS., Maeda AY., Vasami FG., Macedo FL., Suzuki A., Rodrigues SG., Cruz AC., Nunes BT., Medeiros DB., Rodrigues DS., Nunes Queiroz AL., da Silva EV., Henriques DF., Travassos da Rosa ES., de Oliveira CS., Martins LC., Vasconcelos HB., Casseb LM., Simith DB., Messina JP., Abade L., Lourenço J., Carlos Junior Alcantara L., de Lima MM., Giovanetti M., Hay SI., de Oliveira RS., Lemos PS., de Oliveira LF., de Lima CP., da Silva SP., de Vasconcelos JM., Franco L., Cardoso JF., Vianez-Júnior JL., Mir D., Bello G., Delatorre E., Khan K., Creatore M., Coelho GE., de Oliveira WK., Tesh R., Pybus OG., Nunes MR., Vasconcelos PF.
Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015, and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. We performed next-generation sequencing to generate seven Brazilian ZIKV genomes sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Results of phylogenetic and molecular clock analyses show a single introduction of ZIKV into the Americas, which we estimated to have occurred between May and December 2013, more than 12 months before the detection of ZIKV in Brazil. The estimated date of origin coincides with an increase in air passengers to Brazil from ZIKV-endemic areas, as well as with reported outbreaks in the Pacific Islands. ZIKV genomes from Brazil are phylogenetically interspersed with those from other South American and Caribbean countries. Mapping mutations onto existing structural models revealed the context of viral amino acid changes present in the outbreak lineage; however, no shared amino acid changes were found among the three currently available virus genomes from microcephaly cases. Municipality-level incidence data indicate that reports of suspected microcephaly in Brazil best correlate with ZIKV incidence around week 17 of pregnancy, although this correlation does not demonstrate causation. Our genetic description and analysis of ZIKV isolates in Brazil provide a baseline for future studies of the evolution and molecular epidemiology of this emerging virus in the Americas.