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Complete Genome Sequence of Zika Virus Isolated in Mexico, 2016 José Alberto Díaz-Quiñonez,a,b Rocío Peña-Alonso,a Edgar Mendieta-Condado,a Fabiola Garcés-Ayala,a Elizabeth González-Durán,a Noé Escobar-Escamilla,a,e Mauricio Vázquez-Pichardo,a María de la Luz Torres-Rodríguez,a Alma Núñez-León,a Belem Torres-Longoria,a Irma López-Martínez,a Cuitláhuac Ruíz-Matus,c Pablo Kuri-Morales,d José Ernesto Ramírez-Gonzáleza Instituto de Diagnóstico y Referencia Epidemiológicos (InDRE) Dr. Manuel Martínez Báez, Mexico City, Mexicoa; Facultad de Medicina, UNAM, Mexico City, Mexicob; Dirección General de Epidemiología, Mexico City, Mexicoc; Subsecretaría de Prevención y Promoción de la Salud, Mexico City, Mexicod; Escuela Nacional de Ciencias Biológicas, IPN, Mexico City, Mexicoe

Zika virus belongs to the genus Flavivirus, and its spread remains an international public health emergency. In this report, we describe the obtainment and molecular characterization of a complete viral genome through the direct metagenomic analysis from saliva from an autochthonous transmission case in Mexico. Received 3 June 2016 Accepted 6 June 2016 Published 4 August 2016 Citation Díaz-Quiñonez JA, Peña-Alonso R, Mendieta-Condado E, Garcés-Ayala F, González-Durán E, Escobar-Escamilla N, Vázquez-Pichardo M, Torres-Rodríguez MDLL, NúñezLeón A, Torres-Longoria B, López-Martínez I, Ruíz-Matus C, Kuri-Morales P, Ramírez-González JE. 2016. Complete genome sequence of Zika virus isolated in Mexico, 2016. Genome Announc 4(4):e00750-16. doi:10.1128/genomeA.00750-16. Copyright © 2016 Díaz-Quiñonez et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. Address correspondence to José Alberto Díaz-Quiñonez, [email protected], or José Ernesto Ramírez-González, [email protected].

Z

ika virus (ZIKV) is an emerging arbovirus transmitted by Aedes mosquitoes and belongs to the genus Flaviviridae. Most often, signs and symptoms are maculopapular rash, fever, arthralgia, myalgia, headache, and conjunctivitis; edema, sore throat, cough, and vomiting occur less frequently (1). Here, we report the complete genome sequence of a Zika virus strain MEX/InDRE/Sm/2016 directly from the saliva of an autochthonous case. Strain MEX/InDRE/Sm/2016 was identified in the saliva of a 22-year-old woman. Viral RNA was isolated using the QIAamp viral RNA minikit and selectively purified with the RiboMinus eukaryote kit. A single-end library was generated and sequenced using the Ion Torrent platform, and 946,499 reads for MEX/InDRE/Sm/2016 were obtained. The complete genome was assembled using Tmap version 4.2.18, using the sequence of Zika virus strain MRS_OPY_Martinique_PaRi_2015 as a mapping reference (accession no. KU647676.1). A consensus sequence was obtained, with a total length of 10,617 bp and an average coverage of 134⫻ The sequence was annotated and submitted using the NCBI BankIt tool. The obtained sequence contains a single open reading frame (ORF) that encodes a polyprotein that is cleaved into the following structural proteins: capsid (C), premembrane (Pr), membrane (M), and envelope (E), and 8 nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, 2K, NS4B, and NS5). Maximum-likelihood phylogenetic analysis on a genomic scale using the Tamura-Nei substitution model revealed that the strain belongs to the Asian lineage and is related to strains identified in America during the virus dispersion from Southeast Asia. The closest evolutionary relationship was established with the strain causing an outbreak in Martinique at the end of 2015 (2), forming a clade in which the strains identified in Colombia, Panama, and the virus sequenced from the amniotic fluid of a fetus with microcephaly in Brazil (3) in the same season are included. An in silico mutation analysis in the different ORFs revealed different amino

July/August 2016 Volume 4 Issue 4 e00750-16

acid changes: in particular, our sequence presented two mutations observed in the Asian lineage isolated only in the Americas and French Polynesia, those of S17N in the propeptide region of the capsid protein, and M114V in the NS5 protein. The molecular markers that defined relationship with the strain from Martinique were V80T in NS2A and T833A in NS5. Additionally, two amino acid changes were observed only in Zika virus genome from Mexico: A106E in NS3 and H289Q in the NS5 protein. Nucleotide sequence accession number. The assembled complete genome sequence of MEX/InDRE/Sm/2016 was submitted to GenBank with accession no. KU922960. ACKNOWLEDGMENTS We thank all the staff of the Molecular Biology and Virology Departments, InDRE, for technical assistance. No external funding was received for this work. The findings and conclusions in this report are those of the authors and do not necessarily represent the official opinion of the Ministry of Health in Mexico.

REFERENCES 1. Díaz-Quiñonez JA, Escobar-Escamilla N, Wong-Arámbula C, VázquezPichardo M, Torres-Longoria B, López-Martínez I, Ruiz-Matus C, KuriMorales P, Ramírez-González JE. 2016. Asian genotype Zika virus detected in traveler returning to Mexico from Colombia. October 2015. Emerg Infect Dis 22:937–939. http://dx.doi.org/10.3201/eid2205.160190. 2. Piorkowski G, Richard P, Baronti C, Gallian P, Charrel R, LeparcGoffart I, de Lamballerie X. 2016. Complete coding sequence of Zika virus from Martinique outbreak in 2015. New Microbes New Infect 11:52–53. http://dx.doi.org/10.1016/j.nmni.2016.02.013. 3. Calvet G, Aguiar RS, Melo ASO, Sampaio SA, de Filippis I, Fabri A, Araujo ESM, de Sequeira PC, de Mendonça MCL, de Oliveira L, Tschoeke DA, Schrago CG, Thompson FL, Brasil P, dos Santos FB, Nogueira RMR, Tanuri A, de Filippis AMB. 2016. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect Dis 16:653– 660. http://dx.doi.org/10.1016/ S1473-3099(16)00095-5.

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Complete Genome Sequence of Zika Virus Isolated in Mexico, 2016.

Zika virus belongs to the genus Flavivirus, and its spread remains an international public health emergency. In this report, we describe the obtainmen...
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