# First report of Sugarcane bacilliform Guadeloupe A virus and a novel badnavirus infecting sugarcane (Saccharum officinarum) in Côte d'Ivoire

Migninlbin Marcel Ouattara, Cecile Desbiez, Konan Didier Kouame, Grégory

Girardot, Fatogoma Sorho, Mamadou Cherif, Kouakou Yao, Binaté Ble,

Daouda Koné, Alexandra Schoeny

<figure><img src="image_1.png" /></figure>

## ► To cite this version:

Migninlbin Marcel Ouattara, Cecile Desbiez, Konan Didier Kouame, Grégory Girardot, Fatogoma Sorho, et al.. First report of Sugarcane bacilliform Guadeloupe A virus and a novel badnavirus infecting sugarcane (Saccharum officinarum) in Côte d'Ivoire. New Disease Reports, 2024, 49 (1), 10.1002/ndr2.12243. hal-04588416

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# First report of Sugarcane bacilliform Guadeloupe A virus and a novel badnavirus infecting sugarcane (Saccharum officinarum) in Côte d'Ivoire

Migninlbin Marcel Ouattara, Cecile Desbiez, Konan Didier Kouame, Grégory

Girardot, Fatogoma Sorho, Mamadou Cherif, Kouakou Yao, Binaté Ble,

Daouda Koné, Alexandra Schoeny

► To cite this version:

Migninlbin Marcel Ouattara, Cecile Desbiez, Konan Didier Kouame, Grégory Girardot, Fatogoma Sorho, et al.. First report of Sugarcane bacilliform Guadeloupe A virus and a novel badnavirus infecting sugarcane (Saccharum officinarum) in Côte d'Ivoire. New Disease Reports, 2024, 49 (1), pp.e12243. 10.1002/ndr2.12243. hal-04588416

HAL Id: hal-04588416

https://hal.inrae.fr/hal-04588416v1

Submitted on 27 May 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_3.png" /></figure>

# First report of *Sugarcane bacilliform Guadeloupe A virus* and a novel badnavirus infecting sugarcane (*Saccharum officinarum*) in Côte d'Ivoire

M. M. Ouattara<fnref n="1" /> ID

C. Desbiez<fnref n="2" /> ID

K. D. Kouame<fnref n="1" />,<fnref n="3" />

G. Girardot<fnref n="2" />

F. Sorho<fnref n="1" />,<fnref n="3" /> ID

M. Cherif<fnref n="1" />,<fnref n="3" />

K. Yao<fnref n="4" />

B. Ble<fnref n="4" />

D. Koné<fnref n="4" />

A. Schoeny<fnref n="2" />

**Correspondence**

M. M. Ouattara, Wascal/CCBAD-Center of Excellence on Climate Change, Biodiversity and Sustainable Agriculture, Félix Houphouët-Boigny University, 01 BP V 34 Abidjan 01, Côte d'Ivoire. Email: ouattaramign@gmail.com

**Funding information**

SUCRIVOIRE, Grant/Award Number: Convention/3004_2019; CEA-CCBAD; INRAE, EVAg project, Grant/Award Number: H2020 INFRAIA 653316

**KEYWORDS**

Bacilliform Virus, Plant Virology, Sugarcane

A sugarcane sample presenting typical symptoms of *Sugarcane streak mosaic virus* (SCSMV), was collected in the Zuenoula area, Côte d'Ivoire, in April 2022. After total nucleic acid extraction and ribodepletion, the sample was submitted to Illumina paired-end 2x150 sequencing. After contig assembly and Blastn comparison with GenBank sequences, contigs of SCSMV were obtained, however two other contigs had high identity with badnaviruses. By extension of the initial contigs with Geneious 8.1.9, two complete circular sequences were obtained, presenting typical badnavirus organisation with three putative ORFs. One badnavirus (MO210454-1_Z.CI, 7445 nt, GenBank Accession No. OR589411), shared 96% nt identity with isolate WZG (KT186240) of *Sugarcane bacilliform Guadeloupe A virus* (SCBGAV) (Muller et al., 2011), the first detection of this virus in Côte d'Ivoire and in Africa. The second isolate (MO210454-2_Z.CI, 7679 nt, acc. OR589412), shared <75% nt identity in the whole genome with known badnaviruses. The most closely related was *Banana streak UA virus* (NC_015502, 72% identity).

A criteria for species demarcation in the badnaviruses is >20% nucleotide sequence difference in the polymerase (RT + RNAse H) region. In this region, as in the whole genome, MO210454-1_Z.CI shared 94 to 96% identity with isolates of SCBGAV (KT186240 and NC_038382). MO210454-2_Z.CI had 97% and 89% identity, respectively, with the partial sequence of two uncharacterised sugarcane bacilliform virus isolates, YC 273-2 and YC 269-3 (MK632879 and MK632880), collected from sugarcane in China in 2017. It shared less <80% identity with *Banana streak UA virus* (NC_015502) and the tentative badnavirus *Banana streak CA virus* (NC_015506), and <75% identity with the other badnaviruses (Figure 1). Thus, MO210454-2_Z.CI is a tentative novel badnavirus species, also present in China, for which we propose the name *Sugarcane bacilliform Côte d'Ivoire virus* (SCBCIV).

To test the prevalence and diversity of these viruses in Côte d'Ivoire, 106 samples collected in the Zuénoula and Borotou-Koro

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

© 2024 The Authors. *New Disease Reports* published by British Society for Plant Pathology and John Wiley & Sons.

<footnote n="1">¹Wascal/CCBAD-Center of Excellence on Climate Change, Biodiversity and Sustainable Agriculture, Félix Houphouët-Boigny University, Abidjan, Côte d'Ivoire</footnote>

<footnote n="2">²INRAE, Plant Pathology, Montfavet, France</footnote>

<footnote n="3">³UFR Biosciences/Laboratory of Biotechnology, Agriculture and Valorisation of Biological Resources/UPR Plant Physiology and Pathologies, Félix Houphouët Boigny University, Abidjan, Côte d'Ivoire</footnote>

<footnote n="4">⁴Agronomic Department, Field Department, UAI de Zuénoula and Borotou-Koro Sucrivoire, Borotou-Koro, Côte d'Ivoire</footnote>
<figure><img src="image_2.png" /></figure>

# First report of *Sugarcane bacilliform Guadeloupe A virus* and a novel badnavirus infecting sugarcane (*Saccharum officinarum*) in Côte d'Ivoire

M. M. Ouattara<fnref n="1" /> ID

C. Desbiez<fnref n="2" /> ID

K. D. Kouame<fnref n="1" />,<fnref n="3" />

G. Girardot<fnref n="2" />

F. Sorho<fnref n="1" />,<fnref n="3" /> ID

M. Cherif<fnref n="1" />,<fnref n="3" />

K. Yao<fnref n="4" />

B. Ble<fnref n="4" />

D. Koné<fnref n="4" />

A. Schoeny<fnref n="2" />

**Correspondence**

M. M. Ouattara, Wascal/CCBAD-Center of Excellence on Climate Change, Biodiversity and Sustainable Agriculture, Félix Houphouët-Boigny University, 01 BP V 34 Abidjan 01, Côte d'Ivoire. Email: ouattaramign@gmail.com

**Funding information**

SUCRIVOIRE, Grant/Award Number: Convention/3004_2019; CEA-CCBAD; INRAE, EVAg project, Grant/Award Number: H2020 INFRAIA 653316

**KEYWORDS**

Bacilliform Virus, Plant Virology, Sugarcane

A sugarcane sample presenting typical symptoms of *Sugarcane streak mosaic virus* (SCSMV), was collected in the Zuenoula area, Côte d'Ivoire, in April 2022. After total nucleic acid extraction and ribodepletion, the sample was submitted to Illumina paired-end 2x150 sequencing. After contig assembly and Blastn comparison with GenBank sequences, contigs of SCSMV were obtained, however two other contigs had high identity with badnaviruses. By extension of the initial contigs with Geneious 8.1.9, two complete circular sequences were obtained, presenting typical badnavirus organisation with three putative ORFs. One badnavirus (MO210454-1_Z.CI, 7445 nt, GenBank Accession No. OR589411), shared 96% nt identity with isolate WZG (KT186240) of *Sugarcane bacilliform Guadeloupe A virus* (SCBGAV) (Muller et al., 2011), the first detection of this virus in Côte d'Ivoire and in Africa. The second isolate (MO210454-2_Z.CI, 7679 nt, acc. OR589412), shared <75% nt identity in the whole genome with known badnaviruses. The most closely related was *Banana streak UA virus* (NC_015502, 72% identity).

A criteria for species demarcation in the badnaviruses is >20% nucleotide sequence difference in the polymerase (RT + RNAse H) region. In this region, as in the whole genome, MO210454-1_Z.CI shared 94 to 96% identity with isolates of SCBGAV (KT186240 and NC_038382). MO210454-2_Z.CI had 97% and 89% identity, respectively, with the partial sequence of two uncharacterised sugarcane bacilliform virus isolates, YC 273-2 and YC 269-3 (MK632879 and MK632880), collected from sugarcane in China in 2017. It shared less <80% identity with *Banana streak UA virus* (NC_015502) and the tentative badnavirus *Banana streak CA virus* (NC_015506), and <75% identity with the other badnaviruses (Figure 1). Thus, MO210454-2_Z.CI is a tentative novel badnavirus species, also present in China, for which we propose the name *Sugarcane bacilliform Côte d'Ivoire virus* (SCBCIV).

To test the prevalence and diversity of these viruses in Côte d'Ivoire, 106 samples collected in the Zuénoula and Borotou-Koro

This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

© 2024 The Authors. *New Disease Reports* published by British Society for Plant Pathology and John Wiley & Sons.

<footnote n="1">¹Wascal/CCBAD-Center of Excellence on Climate Change, Biodiversity and Sustainable Agriculture, Félix Houphouët-Boigny University, Abidjan, Côte d'Ivoire</footnote>

<footnote n="2">²INRAE, Plant Pathology, Montfavet, France</footnote>

<footnote n="3">³UFR Biosciences/Laboratory of Biotechnology, Agriculture and Valorisation of Biological Resources/UPR Plant Physiology and Pathologies, Félix Houphouët Boigny University, Abidjan, Côte d'Ivoire</footnote>

<footnote n="4">⁴Agronomic Department, Field Department, UAI de Zuénoula and Borotou-Koro Sucrivoire, Borotou-Koro, Côte d'Ivoire</footnote>
<figure><img src="image_4.png" /></figure>

<figure><img src="image_5.png" /><figcaption>**FIGURE 1** Maximum likelihood tree based on a 579 nt fragment in the RT/RNase H region of two sugarcane badnaviruses from Côte d'Ivoire and 11 from recognised or putative badnavirus species. Sequence alignments were performed with MAFFT (https://mafft.cbrc.jp/alignments/software/). Tree reconstruction was performed with MEGA6, using the GTR+G+I substitution model selected with MEGA6. Bootstrap values (n = 500 bootstraps) >50% are indicated for each node. Scale bar represents a genetic distance of 0.2.</figcaption></figure>

<table><caption>**TABLE 1** Detection of badnaviruses in sugarcane samples from the Zuenoula and Borotou Koro production areas</caption><thead><tr><th>Locality</th><th>Collection year</th><th>Number of samples</th><th>Number of positive samples</th></tr></thead><tbody><tr><td rowspan="4">Zuénoula</td><td>2018</td><td>15</td><td>1</td></tr><tr><td>2020</td><td>11</td><td>2</td></tr><tr><td>2022</td><td>11</td><td>4</td></tr><tr><td>2023</td><td>23</td><td>12</td></tr><tr><td rowspan="3">Borotou-Koro</td><td>2019</td><td>25</td><td>0</td></tr><tr><td>2020</td><td>11</td><td>5</td></tr><tr><td>2022</td><td>10</td><td>6</td></tr><tr><td>TOTAL</td><td></td><td>106</td><td>30</td></tr></tbody></table>

sugarcane production sites between 2018 and 2022 were analysed. Some of these plants had accentuated yellowing on the main vein but this symptom appeared on plants that tested positive and negative for badnavirus subsequently. (Figure 2). Total DNA was extracted as described by Gilbertson et al. (1991). Two primers Badna-F 5'-CCATTTGGTYTGAARAATGCTCC-3' and Badna-R 5'-TCCTCCCCATCCNTCCATRCAACC-3', were designed based on Yang et al. (2003) targeting the RT/RNase H region, and 30 samples (28.3%) were positive (Table 1). The 17 samples with strongest PCR amplification were digested with HindIII. Based on the sequences available for MO210454-1_Z.CI and MO210454-2_Z.CI, fragments of 370

nt + 190 nt were expected for SCBGAV and 300 nt + 260 nt for SCBCIV. Sixteen samples had profiles of SCBGAV, and one sample had a mixed infection of SCBGAV and SCBCIV. Five samples with a SCBGAV profile were Sanger sequenced (Gensocreen, France). These five isolates shared 93.5-98.8% identity between themselves and with MO210454-1_Z.CI and other SCBGAV isolates, showing that they were the same species and that the intraspecific diversity of the virus in Côte d'Ivoire is as high as between different countries (data not shown). SCBGAV seems to be more prevalent than SCBCIV in Côte d'Ivoire. Further studies are required to estimate the prevalence and impact of badnaviruses in Côte d'Ivoire.
<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /><figcaption>**FIGURE 1** Maximum likelihood tree based on a 579 nt fragment in the RT/RNase H region of two sugarcane badnaviruses from Côte d'Ivoire and 11 from recognised or putative badnavirus species. Sequence alignments were performed with MAFFT (https://mafft.cbrc.jp/alignments/software/). Tree reconstruction was performed with MEGA6, using the GTR+G+I substitution model selected with MEGA6. Bootstrap values (n = 500 bootstraps) >50% are indicated for each node. Scale bar represents a genetic distance of 0.2.</figcaption></figure>

<table><caption>**TABLE 1** Detection of badnaviruses in sugarcane samples from the Zuenoula and Borotou Koro production areas</caption><thead><tr><th>Locality</th><th>Collection year</th><th>Number of samples</th><th>Number of positive samples</th></tr></thead><tbody><tr><td rowspan="4">Zuénoula</td><td>2018</td><td>15</td><td>1</td></tr><tr><td>2020</td><td>11</td><td>2</td></tr><tr><td>2022</td><td>11</td><td>4</td></tr><tr><td>2023</td><td>23</td><td>12</td></tr><tr><td rowspan="3">Borotou-Koro</td><td>2019</td><td>25</td><td>0</td></tr><tr><td>2020</td><td>11</td><td>5</td></tr><tr><td>2022</td><td>10</td><td>6</td></tr><tr><td>TOTAL</td><td></td><td>106</td><td>30</td></tr></tbody></table>

sugarcane production sites between 2018 and 2022 were analysed. Some of these plants had accentuated yellowing on the main vein but this symptom appeared on plants that tested positive and negative for badnavirus subsequently. (Figure 2). Total DNA was extracted as described by Gilbertson et al. (1991). Two primers Badna-F 5'-CCATTTGGTYTGAARAATGCTCC-3' and Badna-R 5'-TCCTCCCCATCCNTCCATRCAACC-3', were designed based on Yang et al. (2003) targeting the RT/RNase H region, and 30 samples (28.3%) were positive (Table 1). The 17 samples with strongest PCR amplification were digested with HindIII. Based on the sequences available for MO210454-1_Z.CI and MO210454-2_Z.CI, fragments of 370

nt + 190 nt were expected for SCBGAV and 300 nt + 260 nt for SCBCIV. Sixteen samples had profiles of SCBGAV, and one sample had a mixed infection of SCBGAV and SCBCIV. Five samples with a SCBGAV profile were Sanger sequenced (Gensocreen, France). These five isolates shared 93.5-98.8% identity between themselves and with MO210454-1_Z.CI and other SCBGAV isolates, showing that they were the same species and that the intraspecific diversity of the virus in Côte d'Ivoire is as high as between different countries (data not shown). SCBGAV seems to be more prevalent than SCBCIV in Côte d'Ivoire. Further studies are required to estimate the prevalence and impact of badnaviruses in Côte d'Ivoire.
<figure><img src="image_6.png" /><figcaption>**FIGURE 2** Symptoms on sugarcane plants which were collected for badnavirus testing</figcaption></figure>

## ACKNOWLEDGEMENTS

We thank the French Embassy in Côte d'Ivoire and Campus France for a mobility scholarship. This work had financial support from Was-

cal, Sucrivoire and INRAE. Illumina HTS was performed at DSMZ and funded by project EVAg (H2020 INFRAIA 653316).

## ORCID

M. M. Ouattara ID https://orcid.org/0009-0003-6867-508X

C. Desbiez ID https://orcid.org/0000-0001-8691-7423

F. Sorho ID https://orcid.org/0000-0002-6155-6251

## REFERENCES

Gilbertson, R.L., Rojas, M.R., Russell, D.R. & Maxwell, D.P. (1991) Use of the asymmetric polymerase chain reaction and DNA sequencing to determine genetic variability of bean golden mosaic geminivirus in the Dominican Republic. *Journal of General Virology*, **72**, 2843–2848. https://doi.org/10.1099/0022-1317-72-11-2843

Muller, E., Dupuy, V., Blondin, L., Bauffe, F., Daugrois, J.-H., Nathalie, L. et al. (2011) High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. *Virus Research*, **160**, 414–419. https://doi.org/10.1016/j.virusres.2011.06.016

Tamura, K., Stecher, G. & Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. *Molecular Biology and Evolution*, **38**, 3022–3027. https://doi.org/10.1093/molbev/msab120

Yang, I.C., Hafner, G.J., Revill, P.A. & Harding R.M. (2003) Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. *Archives of Virology*, **148**, 1957–1968. https://doi.org/10.1007/s00705-003-0163-0

**How to cite this article:** Ouattara, M.M., Desbiez, C., Kouame, K.D., Girardot, G., Sorho, F., Cherif, M. et al. (2024) First report of *Sugarcane bacilliform Guadeloupe A virus* and a novel badnavirus infecting sugarcane (*Saccharum officinarum*) in Côte d'Ivoire. *New Disease Reports*, **49**, e12243. https://doi.org/10.1002/ndr2.12243
<figure><img src="image_5.png" /><figcaption>**FIGURE 2** Symptoms on sugarcane plants which were collected for badnavirus testing</figcaption></figure>

## ACKNOWLEDGEMENTS

We thank the French Embassy in Côte d'Ivoire and Campus France for a mobility scholarship. This work had financial support from Was-

cal, Sucrivoire and INRAE. Illumina HTS was performed at DSMZ and funded by project EVAg (H2020 INFRAIA 653316).

## ORCID

M. M. Ouattara ID https://orcid.org/0009-0003-6867-508X

C. Desbiez ID https://orcid.org/0000-0001-8691-7423

F. Sorho ID https://orcid.org/0000-0002-6155-6251

## REFERENCES

Gilbertson, R.L., Rojas, M.R., Russell, D.R. & Maxwell, D.P. (1991) Use of the asymmetric polymerase chain reaction and DNA sequencing to determine genetic variability of bean golden mosaic geminivirus in the Dominican Republic. *Journal of General Virology*, **72**, 2843–2848. https://doi.org/10.1099/0022-1317-72-11-2843

Muller, E., Dupuy, V., Blondin, L., Bauffe, F., Daugrois, J.-H., Nathalie, L. et al. (2011) High molecular variability of sugarcane bacilliform viruses in Guadeloupe implying the existence of at least three new species. *Virus Research*, **160**, 414–419. https://doi.org/10.1016/j.virusres.2011.06.016

Tamura, K., Stecher, G. & Kumar, S. (2021) MEGA11: Molecular Evolutionary Genetics Analysis Version 11. *Molecular Biology and Evolution*, **38**, 3022–3027. https://doi.org/10.1093/molbev/msab120

Yang, I.C., Hafner, G.J., Revill, P.A. & Harding R.M. (2003) Sequence diversity of South Pacific isolates of Taro bacilliform virus and the development of a PCR-based diagnostic test. *Archives of Virology*, **148**, 1957–1968. https://doi.org/10.1007/s00705-003-0163-0

**How to cite this article:** Ouattara, M.M., Desbiez, C., Kouame, K.D., Girardot, G., Sorho, F., Cherif, M. et al. (2024) First report of *Sugarcane bacilliform Guadeloupe A virus* and a novel badnavirus infecting sugarcane (*Saccharum officinarum*) in Côte d'Ivoire. *New Disease Reports*, **49**, e12243. https://doi.org/10.1002/ndr2.12243