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Molecular characterization of a novel gammacarmovirus infecting cucurbits in India

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Abstract

In this study, we describe the identification of a new gammacarmovirus infecting Cucurbita pepo plants showing a range of mosaic, stunting, yellowing, and wilting symptoms. The virus had a narrow host range and mostly produced chlorotic and necrotic local lesions in the majority of the tested plants. However, Nicotiana benthamiana showed systemic symptoms under laboratory conditions. Using a combination of Sanger sequencing and rapid amplification of cDNA ends (RACE), the complete genome sequence of the virus was determined to be 4274 nucleotides (nt) in length. Its genome organization is similar to that of members of the genus Gammacarmovirus in the family Tombusviridae, consisting of five overlapping open reading frames (ORFs) encoding p28, replicase, p7A, p7B, and coat protein (CP), respectively. The genome is flanked by short 5′ and 3′ non-coding regions (NCR) at either end. In pairwise comparisons of replicase and CP sequences, the virus showed the highest amino acid sequence identity of 71.55% and 54.86%, respectively, to melon necrotic spot virus (MNSV), the type member of the genus Gammacarmovirus. Since the sequence identity values are below the species demarcation threshold suggested by the International Committee on Taxonomy of Viruses (ICTV), the virus from Cucurbita pepo plants, for which the name "cucurbit carmovirus" (CuCV) is proposed, represents a new species. In phylogenetic analysis based on the replicase and CP amino acid sequences, CuCV clustered with MNSV but formed a distinct branch, further confirming that the virus is a distinct member of the genus Gammacarmovirus.

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Data availability

All the data generated or analyzed during this study are included in this manuscript and the supplimentary data has been attached and the complete genome sequence is deposited in NCBI database with an accession number JX879088 (https://www.ncbi.nlm.nih.gov/nuccore/440454716).

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Acknowledgements

This research was supported by the Department of Biotechnology, Ministry of Science and Technology, India (DBT) India, project code DBT/04/0404/2011/00070 and IPM-CRSP project code EPPA-A-00-04-000216-00/19276-425678.

Funding

Funding was provided by Department of Biotechnology, Ministry of Science and Technology, India (DBT) India, project code DBT/04/0404/2011/00070 and IPM-CRSP project code EPPA-A-00-04-000216-00/19276-425678.

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Author notes

  1. Dileep Kumar Neeraganti and Naga Teja Natra contributed equally.

Authors and Affiliations

  1. Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, 500 019, India

    Dileep Kumar Neeraganti, Naga Teja Natra & Gopinath Kodetham

  2. Department of Plant Pathology, Irrigated Agriculture Research and Extension Center, Washington State University, Prosser, WA, 99350, USA

    Rayapati A. Naidu

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  1. Dileep Kumar Neeraganti
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  2. Naga Teja Natra
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  3. Rayapati A. Naidu
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  4. Gopinath Kodetham
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Contributions

Author GK conceived and designed the work. NTN conducted the experiments, and DKN analysed the data and contributed equally to the work. The first draft of the manuscript was written by DKN and GK, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.

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Correspondence to Gopinath Kodetham.

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Neeraganti, D.K., Natra, N.T., Naidu, R.A. et al. Molecular characterization of a novel gammacarmovirus infecting cucurbits in India. Arch Virol 168, 65 (2023). https://doi.org/10.1007/s00705-022-05643-z

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