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Volume 21, Number 3—March 2015
Research

Nanomicroarray and Multiplex Next-Generation Sequencing for Simultaneous Identification and Characterization of Influenza Viruses

Jiangqin ZhaoComments to Author , Viswanath Ragupathy, Jikun Liu, Xue Wang, Sai Vikram Vemula, Haja Sittana El Mubarak, Zhiping Ye, Marie L. Landry, and Indira HewlettComments to Author 
Author affiliations: Food and Drug Administration, Silver Spring, Maryland, USA (J. Zhao, V. Ragupathy, J. Liu, X. Wang, S.V. Vemula, H.S. El Mubarak, Z. Ye, I. Hewlett); Yale University School of Medicine, New Haven, Connecticut, USA (M.L. Landry)

Main Article

Table 2

Summary of results from NGS data analysis for influenza A(H3N2) and A(H5N1) viruses obtained from the Centers for Disease Control and Prevention

Strain NGS total
contigs/reads Findings Gene segment (length, bp)
PB2
(2,341) PB1
(2,341) PA
(2,233) HA
(1,778) NP
(1,565) NA
(1,413) M
(1,027) NS
(890)
A/Vietnam/1203/ 2004(H5N1) 8/125,438 Length, bp 2,032 1,801 1,841 1,747 1,120 1,259 1,075 894
Read count 7,604 2,019 18,762 16,925 6,490 24,192 20,127 920
A/Minnesota/10/ 2012(H3N2) 8/162,155 Length, bp 2,251 2,192 2,081 1,754 1,556 1,639 1,171 876
Read count 30,002 16,392 19,253 15,194 21,818 8,119 25,879 18,519
A/Vietnam/1203/ 2004(H5N1) and A/Minnesota/10/ 2012(H3N2) 15/150,756 Contigs, H5 2 1 13 14 4 6 7
Length, bp 2,013 2,115 1,815 1,746 1,476 1,193 936
Read count 7,003 6,857 4,359 3,735 854 10,895 15,127
Contigs, H3 15 5 10 11 3 12 8 9
Length, bp 2,530 2,393 1,959 1,465 1,565 1,633 1,103 925
Read count 15,521 6,753 4,113 7,743 13,808 11,147 5,411 6,110

*de novo assembly module was used in CLC Genomics Workbench software version 6.0.2 (CLC bio, Cambridge, MA, USA) for result handing. Minimum contiguous length was set for 800 to assemble the consensus sequences. NGS, next-generation sequencing; PB, polybasic; PA, polymerase; HA, hemagglutinin; NP, nucleoprotein; NA, neuraminidase; M, matrix; NS, nonstructural.

Main Article

Page created: February 18, 2015
Page updated: February 18, 2015
Page reviewed: February 18, 2015
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
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