Complete genome sequences of Zika virus strains isolated from the blood of patients in Thailand in 2014 and the Philippines in 2012

Genome Announcements

Volumn 4, Issue 3, 2016, Pages

  Ellison, D W ^a   Ladner, J T ^b   Buathong, R ^c   Alera, M T ^a   Wiley, M R ^b   Hermann, L ^a   Rutvisuttinunt, W ^a   Klungthong, C ^a   Chinnawirotpisan, P ^a   Manasatienkij, W ^a   Melendrez, M C ^d   Berry, I Maljkovic ^d   Thaisomboonsuk, B ^a   Ong ajchaowlerd, P ^a   Kaneechit, W ^a   Velasco, J M ^a   Tac An, I A ^e   Villa, D ^e   Lago, C B ^a   Roque, V G ^f   Plipat, T ^c   Nisalak, A ^a   Srikiatkhachorn, A ^g   Fernandez, S ^h   Yoon, I K ⁱ   Haddow, A D ^b   Palacios, G F ^b   Jarman, R G ^d   Macareo, L R ^a   more..

^a ARMED FORCES RESEARCH INSTITUTE OF MEDICAL SCIENCES   (Thailand)

^b UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^c MINISTRY OF PUBLIC HEALTH   (Thailand)

^d WALTER REED ARMY INSTITUTE OF RESEARCH   (United States)

^e Cebu City Health Office   (Philippines)

^f DEPARTMENT OF HEALTH   (Philippines)

^g UNIVERSITY OF MASSACHUSETTS MEDICAL SCHOOL   (United States)

^h U S ARMY   (United States)

ⁱ International Vaccine Institute   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 85009948976     PISSN: None     EISSN: 21698287     Source Type: Journal    
DOI: 10.1128/genomeA.00359-16     Document Type: Article

References (15)

1. Calvet G, Aguiar RS, Melo AS, Sampaio SA, de Filippis I, Fabri A, Araujo ES, de Sequeira PC, de Mendonça MC, de Oliveira L, Tschoeke Da SCG, Thompson FL, Brasil P, Dos Santos FB, Nogueira RM, Tanuri A, de Filippis AM. 2016. Detection and sequencing of Zika virus from amniotic fluid of fetuses with microcephaly in Brazil: a case study. Lancet Infect Dis [Epub ahead of print 2016 Feb 17]. http://dx.doi.org/10.1016/S1473-3099(16)00095-5.
2. Haddow AD, Schuh AJ, Yasuda CY, Kasper MR, Heang V, Huy R, Guzman H, Tesh RB, Weaver SC. 2012. Genetic characterization of Zika virus strains: geographic expansion of the Asian lineage. PLoS Negl Trop Dis 6:e1477. http://dx.doi.org/10.1371/journal.pntd.0001477.
3. Kuno G, Chang GJ. 2007. Full-length sequencing and genomic characterization of Bagaza, Kedougou, and Zika viruses. Arch Virol 152: 687-696. http://dx.doi.org/10.1007/s00705-006-0903-z.
4. Buathong R, Hermann L, Thaisomboonsuk B, Rutvisuttinunt W, Klungthong C, Chinnawirotpisan P, Manasatienkij W, Nisalak A, Fernandez S, Yoon IK, Akrasewi P, Plipat T. 2015. Detection of Zika virus infection in Thailand, 2012-2014. Am J Trop Med Hyg 93:380-383. http://dx.doi.org/10.4269/ajtmh.15-0022.
5. Alera MT, Hermann L, Tac-An IA, Klungthong C, Rutvisuttinunt W, Manasatienkij W, Villa D, Thaisomboonsuk B, Velasco JM, Chinnawirotpisan P, Lago CB, Roque VG, Jr, Macareo LR, Srikiatkhachorn A, Fernandez S, Yoon IK. 2015. Zika virus infection, the Philippines, 2012. Emerg Infect Dis 21:722-724. http://dx.doi.org/10.3201/eid2104.141707.
6. Djikeng A, Halpin R, Kuzmickas R, Depasse J, Feldblyum J, Sengamalay N, Afonso C, Zhang X, Anderson NG, Ghedin E, Spiro DJ. 2008. Viral genome sequencing by random priming methods. BMC Genomics 9:5. http://dx.doi.org/10.1186/1471-2164-9-5.
7. Leguia M, Loyola S, Rios J, Juarez D, Guevara C, Silva M, Prieto K, Wiley M, Kasper MR, Palacios G, Bausch DG. 2015. Full genomic characterization of a Saffold virus isolated in Peru. Pathogens 4:816-825. http://dx.doi.org/10.3390/pathogens4040816.
8. MartinM. 2011. Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet.journal 17:10-12. http://dx.doi.org/10.14806/ej.17.1.200.
9. Schmieder R, Edwards R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27:863-864. http://dx.doi.org/10.1093/bioinformatics/btr026.
10. Boisvert S, Raymond F, Godzaridis E, Laviolette F, Corbeil J. 2012. Ray Meta: scalable de novo metagenome assembly and profiling. Genome Biol 13:R122. http://dx.doi.org/10.1186/gb-2012-13-12-r122.
11. Langmead B, Salzberg SL. 2012. Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357-359. http://dx.doi.org/10.1038/nmeth.1923.
12. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009 The sequence alignment/map format and SAMtools. Bioinformatics 25:2078-2079. http://dx.doi.org/10.1093/bioinformatics/btp352.
13. Ladner JT, Beitzel B, Chain PS, Davenport MG, Donaldson EF, Frieman M, Kugelman JR, Kuhn JH, O'Rear J, Sabeti PC, Wentworth DE, Wiley MR, Yu GY, Threat Characterization Consortium, Sozhamannan S, Bradburne C, Palacios G. 2014. Standards for sequencing viral genomes in the era of high-throughput sequencing. mBio 5:e01360-14. http://dx.doi.org/10.1128/mBio.01360-14.
14. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. 2010. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 59: 307-321. http://dx.doi.org/10.1093/sysbio/syq010.
15. Lanciotti RS, Kosoy OL, Laven JJ, Velez JO, Lambert AJ, Johnson AJ, Stanfield SM, Duffy MR. 2008. Genetic and serologic properties of Zika virus associated with an epidemic, Yap state, Micronesia, 2007. Emerg Infect Dis 14:1232-1239. http://dx.doi.org/10.3201/eid1408.080287.