Coat Protein 1 Gene of Indonesian Isolates of Rice Tungro Spherical Virus showed High Divergence with those from other South and South East Asian Regions

Raden Heru Praptana1, Adyatma Irawan Santosa2, *, Rahmini Rahmini1, Wasis Senoaji1, Nur Rosida1, Danarsi Diptaningsari1, Affandi Affandi3, Riska Riska3, Y. Andi Trisyono2, Sedyo Hartono2
1 Research Center for Food Crops, National Research and Innovation Agency, Bogor, Indonesia
2 Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Flora no. 1, Sleman, Yogyakarta 55281, Indonesia
3 Research Center for Horticultural and Estate Crops, National Research and Innovation Agency, Bogor, Indonesia

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© 2023 Praptana et al.

open-access license: This is an open access article distributed under the terms of the Creative Commons Attribution 4.0 International Public License (CC-BY 4.0), a copy of which is available at: This license permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

* Address correspondence to this author at the Department of Plant Protection, Faculty of Agriculture, Universitas Gadjah Mada, Jl. Flora no. 1, Sleman, Yogyakarta, 55281, Indonesia; E-mail:



Tungro, an important viral disease in rice, is a co-infection of rice tungro bacilliform virus (RTBV) and rice tungro spherical virus (RTSV). Severe symptoms were reported in rice fields on two major islands in Indonesia: Jawa (Magelang District) and Sulawesi (Sidrap District).


Sequences of global isolates currently registered in NCBI GenBank were examined with two new Indonesian isolates to understand the phylogeny of RTSV based on different genome regions as well as to spot the gap in the molecular data of Indonesian isolates.


Transmission test of RTSV using the vector green leaf hopper was performed, and then the complete sequences of coat protein 1 (CP1) gene of Magelang and Sindrap districts were molecularly studied using MEGA X software and Recombination Detection Program.


The obtained complete sequence of coat protein 1 (CP1) gene of Magelang-7 (OQ426495) and Sindrap-9 (OQ426496) isolates were aligned with 39 isolates in NCBI GenBank. Sequences of other isolates in GenBank were also retrieved and then aligned according to six individual Open Reading Frames (ORFs) and ‘Full ORF’. Recombination analysis detected significant signals in the genomes of one partially and four fully sequenced isolates. Phylogenetic study also confirmed the frequent recombination among RTSV isolates clustered in two geographically separated groups: South East Asia and South Asia.


Although the available data is still rudimentary, this study demonstrated that the CP1 gene of 21 isolates from different regions of Indonesia was highly identical among themself but divergent with isolates from other countries. Therefore, deep molecular comprehension on Indonesian isolates is necessary to manage the recurrent Tungro spread in the country.

Keywords: Identity matrix, Isolates clustering, Phylogenetic tree, Recombinant isolates, Viral disease, Virus evolution.