Weeds commonly grow along with cultivated plants and may act as reservoir hosts of various vectors and plant viruses (Varma and Malathi 2003; Hull 2014). Cotton leaf curl Gezira virus (CLCuGeV, genus Begomovirus, family Geminiviridae) is one of the begomoviruses causing cotton leaf curl disease (CLCuD), which is as a serious threat to cotton production around the world (Varma and Malathi 2003; Sattar et al. 2013). CLCuGeV was first reported from Africa in 2002 (Idris and Brown 2002) and has a circular single-stranded monopartite DNA genome of 2.7 kb (Brown et al. 2015). The natural hosts of CLCuGeV are mostly limited to wild or crop species of Malvaceae (Tahir et al. 2011; Leke et al. 2013; Bananej et al. 2021b; Salari et al. 2021). CLCuGeV in association with tomato leaf curl betasatellite is recently reported from Malva sylvestris plants in Iran (Bananej et al. 2021b). However, CLCuGeV has been shown to infect also papaya (Khan et al. 2012; Bananej et al. 2021a), tomato (Al-Shihi et al. 2017), pepper and melon (Gambley et al. 2020), sunflower (Salari et al. 2021) and Amaranthus sp. (GenBank Accession no. MN381116; unpublished). Like other begomoviruses, CLCuGeV is transmitted by whiteflies of the Bemisia tabaci species complex (Ghanim 2014; Shahmohammadi et al. 2022). To date, 12 strains of CLCuGeV, including CLCuGeV-Egypt (-EG), -Niger (-NE), -Sudan (-SD), -Cameroon (-CM), -Cairo (-Ca), -Burkina Faso (-BF), -Hollyhock (-Ho), -Lysoka (-Ly), -Madagascar (-MG), -Mali (-ML), -Okra (-OK), and -Al-Batinah (-AB), have been identified (Al-Shihi et al. 2017; ICTV Online 2021), but merging of some strains according to the demarcation criterium of higher than 94% nucleotide identity for strains is proposed (Al-Shihi et al. 2017).

In 2015, nine Chesseweed mallow (Malva parviflora) samples showing leaf curling and yellowing were collected close to tomato fields in Dhi-Qar, Iraq, and subjected to total DNA isolation by a CTAB method (Doyle and Doyle 1987). In order to identify the begomoviruses associated with the symptoms in the collected samples, PCR was performed using the begomovirus-specific degenerate primers PAL1v1978/PAR1c496 (Rojas et al. 1993) and a fragment of 1.4 kb was amplified for four of the samples. To test the possible presence of tomato yellow leaf curl virus (TYLCV) in PCR-positive samples, a subsequent PCR was performed using a TYLCV-specific primer pair (V1 (CP) Forward/V1 (CP) Reverse), which revealed TYLCV infection of three samples (Al-Waeli et al. 2017). For the sample testing negative for TYLCV, circular viral DNA was amplified by rolling circle amplification (RCA) using a Templiphi RCA Kit (GE Healthcare, USA). The RCA product was digested with a range of restriction enzymes, including EcoRI, BamHI, SalI and PstI, yielding a fragment with the expected size of ~ 3 kb by BamHI. The purified fragment was cloned into pBluescript II KS (+) followed by transformation into Escherichia coli DH5α competent cells and sequencing of the complete viral genome in both directions. The presence of a betasatellite was proven by PCR amplification of a 1.3 kb fragment using the primer pair Beta01/Beta02 (Briddon et al. 2002), while no amplicon was obtained for alphasatellites when PCR was performed using the primer pairs DNA101/DNA102 and UN101/UN102 (Bull et al. 2003).

BLASTn searches of the assembled full genome sequence of 2777 nucleotides (nts) showed highest nucleotide identities with isolates of CLCuGeV. Pairwise nt sequence comparisons of the identified Iraqi CLCuGeV isolate (IQ:Dhi:Malva-90:15; GenBank Accession no. ON209402) with other previously reported CLCuGeV isolates using SDT 1.2 software (Muhire et al. 2014) revealed the highest nt identity at 98.2% with an Israeli whitefly isolate of CLCuGeV collected from squash plants (GenBank Accession no. KT099132). High nt identities were also shared with isolates of the strains CLCuGeV-Egypt (95.6–95.9%), including isolates from Pakistan and Iran (FR751143, FR751145, MN328258, MN175235) and CLCuGeV-Cameroon (HE793429, FM210276) (94.0-94.7%; Fig. S1). A neighbour-joining phylogenetic analysis based on the complete nucleotide sequence of IQ:Dhi:Malva-90:15 and isolates of different CLCuGeV strains using MEGA 7 (Kumar et al. 2016) revealed that IQ:Dhi:Malva-90:15 grouped with the isolate from Israel (KT099132) in a distinct branch closely related to the Egypt and Cameroon strain groups (Fig. 1). In a previous study, a merge of the strains Sudan, Cairo, Egypt, Cameroon, Okra, Burkina Faso and Niger was proposed (Al-Shihi et al. 2017). Our results confirmed the proposal as they all have identity values exceeding 94%. Analysis of recombination in the genome of IQ:Dhi:Malva-90:15 using RDP4 (Martin et al. 2015) showed that the Iraqi isolate has the evidence of a recombination event (supported by all seven used methods) in its genome, in which CLCuGeV-Hollyhock and an isolate from Oman (HF536716) were identified as putative major and minor parents, respectively (P = 3.20 × 10− 10 − 8.29 × 10− 20). The recombinant region is of ~ 450 nts (nucleotides 1005–1450) covering the gene region of cp/ren/trap. While it seems that CLCuGeV is circulating in many countries in the Middle East (Tahir et al. 2011; Khan et al. 2012; Idris et al. 2014), to our knowledge, this is the first report of CLCuGeV from Iraq. As this virus was identified from a weed close to a tomato field, further studies are required to investigate the incidence of CLCuGeV on other crop hosts, such as tomato, as well as the geographic distribution.

Fig. 1
figure 1

Neighbour-joining phylogenetic tree reconstructed using MEGA 7 software based on complete nucleotide sequences of isolates of different strains of cotton leaf curl Gezira virus (CLCuGeV). The strain of each isolate is shown in parenthesis. The host and origin of isolates are shown in the tree. The close relatives tomato leaf curl Madagascar virus (ToLCMGV, AJ865338) and tomato leaf curl Comoros virus (ToLCKMV, AM701759) were used as outgroups. Bootstrap values higher than 70 are shown at each node. The Iraqi isolate is shown in bold green text

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