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Volume 22, Number 10—October 2016

Distinct Zika Virus Lineage in Salvador, Bahia, Brazil

Samia N. Naccache1, Julien Thézé1, Silvia I. Sardi, Sneha Somasekar, Alexander L. Greninger, Antonio C. Bandeira, Gubio S. Campos, Laura B. Tauro, Ester C. Sabino, Oliver G. Pybus, and Charles Y. ChiuComments to Author 
Author affiliations: University of California San Francisco, San Francisco, California, USA (S.N. Naccache, S. Somasekar, C.Y. Chiu); University of California San Francisco–Abbott Viral Diagnostics and Discovery Center, San Francisco (S.N. Naccache, S. Somasekar, C.Y. Chiu); University of Oxford, Oxford, UK (J. Thézé, N.R. Faria, O.G. Pybus); Federal University of Bahia, Salvador, Brazil (S.I. Sardi, G.S. Campos); University of Washington, Seattle, Washington, USA (A.L. Greninger); Hospital Alianca, Salvador (A.C. Bandeira); Gonçalo Moniz Research Center–Oswaldo Cruz Foundation, Salvador (L.B. Tauro); Evandro Chagas Institute, Ananindeua, Brazil (N.R. Faria)

Main Article


Clinical information for isolates from serum samples of patients with acute symptomatic Zika virus infection*

Isolate Patient age, y/sex Collection date† Genbank accession no. Zika virus RT-PCR Zika virus qRT-PCR Ct Viral load, copies/ mL 160-nt single-end metagenomic reads
250-nt paired-end Zika virus–specific enrichment
Genome recovery, %‡ Mean fold coverage Genome recovery, %‡ Mean fold coverage
Bahia01 72/F 2015 May 16 KX101066 Pos 34.6 1,042 23.1 0.4 65.3 16,288.2
Bahia02 37/M 2015 May 5 KX101060 Pos 32.5 4,086 26.0 0.4 73.4 20,045.8
Bahia03 35/M 2015 May 5 KX101061 Pos 32.8 3,272 1.1 0.0 77.7 220.0
Bahia04 40/M 2015 Jun 1 KX101062 Pos 34.1 1,464 5.1 0.1 42.0 4,659.5
Bahia05 U/M 2015 Dec 10 KX101063 Pos 33.7 1,901 5.0 0.1 42.8 8,547.5
Bahia07 37/F 2015 Aug 29 KU940228 Pos 13.7 9.1 × 108 100 3,603.5 ND ND
Bahia08 U/M 2015 Jul 15 KU940227 Pos 33.3 2,470 75.1 9.2 84.9 23,805.1
Bahia09 40/F 2015 Apr 25 KU940224 Pos 29.9 23,121 99.98 41.5 ND ND
Bahia11 40/F 2015 Apr 27 KX101064 Pos Neg
(no Ct) NA 27.8 0.9 64.0 28,704.1
Bahia12 36/M 2015 May 7 KX101067 Pos 34.2 1,327 11.2 0.2 50.4 10,461.8
Bahia15 U/M 2016 Jan 25 KX101065 Pos Neg
(no Ct) NA 4.6 0.2 45.4 3,706.8

*Ct, cycle threshold; NA, not applicable; ND, not done; Neg, negative; Pos, positive; qRT-PCR, quantitative reverse transcription PCR; RT-PCR, reverse transcription PCR; U, unknown.
†Samples were collected from Salvador in Bahia, Brazil, except for Bahia05, which was collected in Camaçari, Bahia, Brazil.
‡Assumes a genome size of 10,676 nt, the size of the prototype Brazilian Zika virus strain SPH2015 (KU321639).

Main Article

1These first authors contributed equally to this article.

Page created: September 20, 2016
Page updated: September 20, 2016
Page reviewed: September 20, 2016
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