First report of garlic mite-borne filamentous virus (GarMbFV) infecting garlic (Allium sativum L.) in India

Abstract

During January 2021, mild mosaic-related symptoms
caused by a group of viruses were observed on the leaves
of garlic cultivar Yamuna Safed-3 (G-282). The electron
microscopy of infected leaves revealed the presence of filamentous
shape virus ranging 700 to 800 nm in size. To
identify the virus particles, total RNA of the symptomatic
leaf samples were subjected to RT PCR targeting Allexivirus
genus using degenerate primers (Baranwal et al. 2011) and
analyzed using Target-seq metagenomics approach. cDNA
library was prepared for target sequence metagenomics using
amplified PCR product. Out of 19,442,868 reads generated
using Illumina Novaseq 6000 platform, low-quality reads
were removed, and de novo assembly of contigs was performed.
Searching the protein databases using BLASTX,
resulted in identification of 31 contigs with identity ranging
82.14 – 96.66% to garlic mite-borne filamentous virus.
Furthermore, contigs sharing identity with other allexiviruses
(garlic virus A-E, garlic virus X and blackberry virus
E) were also identified from the assembly. GarMbFV has
been earlier detected in Japan, Argentina, Brazil and South
Korea (Oliveira et al. 2014). The presence of GarMbFV
was confirmed with RT PCR using GarMbFV coat protein
specific primer with an amplification of ~ 760 bp (Fayad-
André et al. 2011). The obtained amplicons were sequenced
bidirectionally and deposited in GenBank under accession
Nos. MZ353585 to MZ353588. The resulting sequences
of the Indian GarMbFV isolate shared 89.9%– 99.30%
and 89.0%– 99.30% identity at nucleotide and amino
acid levels, respectively, with other GarMbFV sequences
reported globally (ST. 1). Phylogenetic analysis revealed,
that GarMbFV Indian isolate shared the same clade with
GarMbFV sequence from Argentina (NC_038864) and Brazil
(KF955571- KF955574) (Oliveira et al. 2014) (SF. 1).
Our results indicate GarMbFV as one of the possible causal
agents for the mild mosaic-like symptoms in garlic similar to
previous reports of other allexiviruses from India (Prajapati
et al. 2021). To the best of our knowledge, this is the first
evidence of GarMbFV in India. However, Koch's postulate
studies are needed to confirm the status of GarMBFV as
the causal agent of the mild mosaic like symptoms in garlic.
Moreover, nation-wide survey to study the distribution,
symptom severity, genetic diversity of GarMBFV warrant
future investigation for risk assessment of GarMBFV to garlic
production in India.

Full text

Vol.:(0123456789)
1 3
Journal of Plant Pathology
https://doi.org/10.1007/s42161-022-01031-3
DISEASE NOTE
First report ofgarlic mite‑borne filamentous virus(GarMbFV) infecting
garlic (Allium sativum L.) inIndia
AakanshaManav1· MalyajR.Prajapati1· JitenderSingh1 · PankajKumar1· VirendraKumarBaranwal2
Received: 30 September 2021 / Accepted: 7 January 2022
© The Author(s) under exclusive licence to Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2022
Keywords Allium sativum L.· Allexivirus· Garlic mite-borne filamentous· Target-seq metagenomics· Phylogenetics
During January 2021, mild mosaic-related symptoms
caused by a group of viruses were observed on the leaves
of garlic cultivar Yamuna Safed-3 (G-282). The electron
microscopy of infected leaves revealed the presence of fil-
amentous shape virus ranging 700 to 800nm in size. To
identify the virus particles, total RNA of the symptomatic
leaf samples were subjected to RT PCR targeting Allexivirus
genus using degenerate primers (Baranwal etal.2011) and
analyzed using Target-seq metagenomics approach. cDNA
library was prepared for target sequence metagenomics using
amplified PCR product. Out of 19,442,868 reads generated
using Illumina Novaseq 6000 platform, low-quality reads
were removed, and de novo assembly of contigs was per-
formed. Searching the protein databases using BLASTX,
resulted in identification of 31 contigs with identity rang-
ing 82.14 – 96.66% to garlic mite-borne filamentous virus.
Furthermore, contigs sharing identity with other allexivi-
ruses (garlic virus A-E, garlic virus X and blackberry virus
E) were also identified from the assembly. GarMbFV has
been earlier detected in Japan, Argentina, Brazil and South
Korea (Oliveira etal.2014). The presence of GarMbFV
was confirmed with RT PCR using GarMbFV coat protein
specific primer with an amplification of ~ 760bp (Fayad-
André etal.2011). The obtained amplicons were sequenced
bidirectionally and deposited in GenBank under accession
Nos. MZ353585 to MZ353588. The resulting sequences
of the Indian GarMbFV isolate shared89.9%– 99.30%
and 89.0%– 99.30% identity at nucleotide and amino
acid levels, respectively, with other GarMbFV sequences
reported globally (ST. 1). Phylogenetic analysis revealed,
that GarMbFV Indian isolate shared the same clade with
GarMbFV sequence from Argentina (NC_038864) and Bra-
zil (KF955571- KF955574) (Oliveira etal.2014) (SF. 1).
Our results indicate GarMbFV as one of the possible causal
agents for the mild mosaic-like symptoms in garlic similar to
previous reports of other allexiviruses from India (Prajapati
etal.2021). To the best of our knowledge, this is the first
evidence of GarMbFV in India. However, Koch's postulate
studies are needed to confirm the status of GarMBFV as
the causal agent of the mild mosaic like symptoms in gar-
lic. Moreover, nation-wide survey to study the distribution,
symptom severity, genetic diversity of GarMBFV warrant
future investigation for risk assessment of GarMBFV to gar-
lic production in India.
Supplementary information The online version contains supplemen-
tary material available at https:// doi. org/ 10. 1007/ s42161- 022- 01031-3.
Acknowledgements The authors acknowledge the Vice Chancellor,
Sardar Vallabhbhai Patel University of Agriculture and Technology,
Meerut-250110, Uttar Pradesh, Bioinformatics facility, Department of
Biotechnology, India for providing financial support and the facilities
to carry out this research work.
Declarations
Informed consent Informed consent was obtained from all individual
participants included in the study.
Research involving animal participants No animal experimental pro-
cedures were used in this study.
Conflict of interest The authors declare that they have no conflict of
interest.
* Jitender Singh
jeets80@gmail.com
1 College ofBiotechnology, Sardar Vallabhbhai Patel
University ofAgriculture andTechnology, Uttar Pradesh,
Meerut250110, India
2 Division ofPlant Pathology, ICAR-Indian Agricultural
Research Institute, NewDelhi110012, India

Journal of Plant Pathology
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