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. 2023 Mar 14;15(3):743.
doi: 10.3390/v15030743.

Genome Characterisation of the CGMMV Virus Population in Australia-Informing Plant Biosecurity Policy

Joanne Mackie  1   2 , Paul R Campbell  3 , Monica A Kehoe  4 , Lucy T T Tran-Nguyen  5 , Brendan C Rodoni  1   2 , Fiona E Constable  1   2
Affiliations

Genome Characterisation of the CGMMV Virus Population in Australia-Informing Plant Biosecurity Policy

Joanne Mackie et al. Viruses. .

Abstract

The detection of cucumber green mottle mosaic (CGMMV) in the Northern Territory (NT), Australia, in 2014 led to the introduction of strict quarantine measures for the importation of cucurbit seeds by the Australian federal government. Further detections in Queensland, Western Australia (WA), New South Wales and South Australia occurred in the period 2015-2020. To explore the diversity of the current Australian CGMMV population, 35 new coding sequence complete genomes for CGMMV isolates from Australian incursions and surveys were prepared for this study. In conjunction with published genomes from the NT and WA, sequence, phylogenetic, and genetic variation and variant analyses were performed, and the data were compared with those for international CGMMV isolates. Based on these analyses, it can be inferred that the Australian CGMMV population resulted from a single virus source via multiple introductions.

Keywords: cucumber green mottle mosaic virus; genetic diversity; median-joining network.

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Conflict of interest statement

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of the data; in the writing of the manuscript; or in the decision to publish the results.

Figures

Figure 1
Figure 1
Sequence Demarcation Tool matrix showing percent pairwise nucleotide similarity for the full coding sequence regions of cucumber green mottle mosaic virus genomes from Australian and seed interception samples.
Figure 2
Figure 2
Sequence Demarcation Tool matrix showing percent pairwise nucleotide similarity for the full coding sequence region genomes of Australian, seed interception and global cucumber green mottle mosaic virus isolates. Colour strips on edges denote isolate collection region: Asia—red, Australia—green, Europe—black, Middle East—orange, North America—blue, and unknown isolates (seed interceptions)—grey.
Figure 3
Figure 3
(A) Bayesian maximum-clade-credibility (mcc) tree estimated for Australian seed intercepts and publicly available cucumber green mottle mosaic virus (CGMMV) genomes using the complete coding region nucleotide sequences. Background colours identify the main clades. Key identifies country of origin for each accession. (B) Clade 2C containing all Australian isolates is presented. The mcc was created using BEAST v1.10.4 [44] using analysis settings: model—Tamura–Nei; rates among sites—gamma distributed with invariant sites. Tip times correspond to the virus sampling date. The posterior probability values are shown on tree branches.
Figure 4
Figure 4
Bayesian maximum-clade-credibility tree estimated for the complete coding region nucleotide sequences of all Australian cucumber green mottle mosaic virus (CGMMV) isolates in sub-clade 2C and seed interception isolates in sub-clades 2C and 2D. The tree was created using BEAST v1.10.4 [44] using the following analysis settings: model—Tamura–Nei; rates among sites—gamma distributed with invariant sites. Tree scale—branch lengths measured by number of substitutions per site. Branch values are posterior probabilities of having a changepoint. Isolate hosts are shown using node symbols (key included).
Figure 5
Figure 5
Median-joining network constructed with PopART 1.7, using the full coding sequence of the 80 cucumber green mottle mosaic virus isolates from Australia and other global regions that are placed in Groups III, IV and V of the Bayesian maximum-clade-credibility tree (Figure 4). Node size is proportional to the number of variants. Sequence node colours correspond to the collection regions of isolates. Hatch marks represent the number of single nucleotide variants between black nodes. Cluster 1 accessions: MH271421.1 (CG015), MH427279.1 (CGMMV-NT), NSW-2019-01, NSW-2020-01, NT-2014-02, NT-2014-03, NT-2015-01, NT-2016-01, NT-2016-02, NT-2017-01, NT-2017-02, NT-2017-03, NT-2019-01, NT-2019-02, NT-2019-03, NT-2019-04, NT-2019-05, NT-2019-06, NT-2019-07, NT-2019-08, NT-2019-09, NT-2019-10, NT-2020-01, NT-2020-02, NT-2020-03, NT-2020-04, NT-2020-05, QLD-2018-01 and SI-2015-01. Cluster 2 accessions: KY115174.1 (WA-1), MW430119.1 (WA-2), MW430120.1 (WA-3), MW430121.1 (WA-4), MW430122.1 (WA-5), MW430123.1 (WA-6), MW430124.1 (WA-7), MW430125.1 (WA-8), QLD_2019_01, QLD_2019_02, SA_2019_01, SA_2019_02, SA_2019_03, SA_2019_04 and SA_2020_01. Cluster 3 accessions: KP772568.1, MH271408.1, MH271410.1, MH271412.1, MH271419.1, MH271441.1, MT184941.1, NT_2015_02, QLD_2015_01, SI_2016_01 and SI_2016_02. Cluster 4 accessions: AB015146.1, GQ277655.1, MF510463.1, MF510464.1, MF510465.1, MF510466.1, MF510467.1, MF510468.1, MF510469.1 and MZ272459.1. Cluster 5 accessions: MH271409.1, MH271444.1, MT184942.1, MT184943.1 and MT184944.1. Cluster 6 accessions: MH271442.1, MZ272454.1, MZ272455.1, MZ272456.1, MZ272457.1, MZ272458.1, MZ272460.1, MZ272461.1, MZ272462.1 and MZ272463.1.
Figure 6
Figure 6
Median-joining networks constructed with PopART 1.7 for movement (A) and coat (B) proteins using global and Australian and seed interception cucumber green mottle mosaic virus isolates. Node size is proportional to the number of variants. Sequence node colours correspond to the collection regions of isolates. Hatch marks represent the number of single nucleotide variants between nodes.
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