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Deep sequencing of banana bract mosaic virus from flowering ginger (Alpinia purpurata) and development of an immunocapture RT-LAMP detection assay

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Abstract

Banana bract mosaic virus (BBrMV) has never been reported in banana plants in Hawaii. In 2010, however, it was detected in a new host, flowering ginger (Alpinia purpurata). In this study, we characterize the A. purpurata isolate and study its spread in flowering ginger in Hawaii. A laboratory study demonstrated that BBrMV could be transmitted from flowering ginger to its natural host, banana, therefore raising a serious concern about the potential risk to the rapidly growing banana industry of Hawaii. To quickly monitor this virus in the field, we developed a robust immunocapture reverse transcription loop-mediated isothermal amplification (IC-RT-LAMP) assay. Deep sequencing of the BBrMV isolate from A. purpurata revealed a single-stranded RNA virus with a genome of 9,713 nt potentially encoding a polyprotein of 3,124 aa, and another predicted protein, PIPO, in the +2 reading-frame shift. Most of the functional motifs in the Hawaiian isolate were conserved among the genomes of isolates from one found in the Philippines and India. However, the A. purpurata isolate had an amino acid deletion in the Pl protein that was most similar to the Philippine isolate. Phylogenetic analysis of an eastern Pacific subpopulation that included A. purpurata was closest in genetic distance to a Southeast Asian subpopulation, suggesting frequent gene flow and supporting the hypothesis that the A. purpurata isolate arrived in Hawaii from Southeast Asia.

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Acknowledgments

This work was supported in part by grants from the National Natural Science Foundation of China (31300118), the President Foundation of the Guangdong Academy of Agricultural Sciences (201306), the National Institute of Food and Agriculture, US Department of Agriculture, Hatch HAW09025-H (1001478), and the U.S. Department of Agriculture, Agricultural Research Service (58-5320-4-012).

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Authors and Affiliations

  1. Department of Plant and Environmental Protection Sciences, College of Tropical Agriculture and Human Resources, University of Hawaii, Honolulu, HI, USA

    Jingxin Zhang, Wayne B. Borth, Kishore K. Dey, Michael J. Melzer & John S. Hu

  2. Key Laboratory of New Technique for Plant Protection in Guangdong, Institute of Plant Protection, Guangdong Academy of Agricultural Sciences, Guangzhou, China

    Jingxin Zhang, Birun Lin, Huifang Shen, Xiaoming Pu & Dayuan Sun

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  1. Jingxin Zhang
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  2. Wayne B. Borth
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  9. John S. Hu
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Correspondence to John S. Hu.

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Funding

This study was funded by grants from the National Natural Science Foundation of China (31300118), the President Foundation of the Guangdong Academy of Agricultural Sciences (201306), the National Institute of Food and Agriculture, US Department of Agriculture, Hatch HAW09025-H (1001478), and the US Department of Agriculture, Agricultural Research Service (58-5320-4-012).

Conflict of interest

Author Jingxin Zhang declares that he has no conflict of interest. Author Wayne Borth declares that he has no conflict of interest. Author Birun Lin declares that he has no conflict of interest. Author Kishore Dey declares that he has no conflict of interest. Author Michael Melzer declares that he has no conflict of interest. Author Huifang Shen declares that she has no conflict of interest. Author Xiaoming Pu declares that he has no conflict of interest. Author Dayuan Sun declares that he has no conflict of interest. Author John Hu declares that he has no conflict of interest.

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Zhang, J., Borth, W.B., Lin, B. et al. Deep sequencing of banana bract mosaic virus from flowering ginger (Alpinia purpurata) and development of an immunocapture RT-LAMP detection assay. Arch Virol 161, 1783–1795 (2016). https://doi.org/10.1007/s00705-016-2830-y

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