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Plant Science Today (PST)

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Early Access

Genetic recombination and diversity analysis reveal novel strain of Citrus tristeza virus (Closterovirus tristezae) in Khasi mandarin growing region of Assam

DOI
https://doi.org/10.14719/pst.7546
Submitted
31 January 2025
Published
19-08-2025
Versions

Abstract

Northeast (NE) India, a hotspot for citrus biodiversity, is facing a serious threat from the Closterovirus tristezae (CTV). A devastating CTV transmitted by the brown citrus aphid (Toxoptera citricida). This pathogen has led to the decline of over one million citrus trees across India, threatening the region’s citrus industry. CTV is characterised by flexuous, filamentous virions (2000×11 nm) and a positive-sense, single-stranded RNA genome (~19.3 kb) encoding 12 open reading frames (ORFs) and approximately 19 putative proteins. To assess the prevalence and genetic diversity of CTV, a systematic survey was conducted in Khasi mandarin (Citrus reticulata) orchards across four districts of Assam: Kamrup Metro, Karbi Anglong, Kamrup Rural and Goalpara. Infected trees exhibited a spectrum of disease symptoms, including decline, chlorosis, leaf yellowing, poor growth and stunting. Disease incidence was determined using Direct Antigen Coated-Enzyme Linked Immunosorbent Assay (DAC-ELISA) and percent disease incidence, revealing 68.2 % overall infection rate. Genetic characterization of 19 CTV isolates, based on a 404-nt fragment of the 5’ ORF1a, unveiled substantial sequence variability, with pairwise nucleotide identities ranging from 85–100 %. Phylogenetic reconstruction grouped these isolates into five distinct genogroups, underscoring significant intra-farm genetic diversity within citrus orchards. Recombination analysis using RDP4 software identified multiple recombinant isolates (BHKM-1, ASKM-1, ASKM-2, MKM-2 and RTKM-1), with BHKM-6 as the major parent and MB-3 as a minor parent contributing to recombination events. These findings provide critical insights into the genetic landscape of CTV in Northeastern (NE) India, emphasising the need for targeted disease management strategies to mitigate further citrus decline.

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