Review Reports - Epidemiology of Cocoa Swollen Shoot Disease (CSSD) on Rehabilitated Cocoa Farms in South-Western Côte d’Ivoire

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This paper from Kouakou et al describes interesting results regarding reinfection with swollen shoot disease in plots that have recently been rehabilitated in the Nawa region of Côte d’Ivoire. The most significant findings relate to molecular epidemiology, including the detection of asymptomatic trees infected 18 metres from the centre of the outbreaks, which will enable the updating of recommendations for trees removal when outbreaks are observed.

However, the analyses carried out are not particularly convincing, as they lack comparisons with unimproved control genotypes. The incidence of the disease probably depends as much on the genotypes used and, above all, on the proximity of infected plots as it does on the rehabilitation technology. Furthermore, the comparative results between the three technologies are not particularly surprising, given that the mature trees from infected areas were not tested for the presence of the virus prior to grafting.

It is also somewhat risky to present results without mentioning the cocoa genotypes observed. Surprisingly, clones are only selected for their productivity, the butter quality and the resistance to black pod disease but not the tolerance to Swollen shoot. Furthermore, the hybrids are not described in any greater detail than as ‘improved coca planting material’. It would have been interesting to know their genotypes for the clones and the hybrids so as to be able to make comparisons with other publications. Just a code number is not sufficient to publish this work.

Specific comments

The lines are not numbered, which makes it very difficult to list the corrections to be taken into account

Page 2 replace “a group of Badnavirus species” by “ a complex of Badnavirus species”

Page 4: The description of the PCR mix must specify the final concentrations used for each component ; simply stating the volume of a solution whose concentration is unknown is not sufficient.

The definition given for prevalence rate and incidence rate simply refer to prevalence and incidence. These definitions should be given earlier when these terms are introduced page 3

Page 6:

To which year of observation do the values in Table 1 correspond?

the repartition of infected plots per technology does not indicate the rate of infection depending of the technology, it would be more appropriate to calculate, for each technology, the number of infected plots as a The incidence of the disease probably depends as much on the genotypes used as on the rehabilitation technology; it is therefore somewhat risky to present results without mentioning the cocoa genotypes observed. proportion of the total number of plots.

Is there a link between the GVV plots monitored for yield (68 plots) and the plots presented in table 1 (57 plots).

“No significant difference was found for cocoa yield be-tween symptomatic and asymptomatic plots when considering the entire cocoa plot irrespective of the cocoa variety and technology applied” but the only observed technology for the yield is the GVV technology of rehabilitation.

Page 7

What does mean “the required number of tree infected plots”

Figure 5B, the calculation of the severity score per clone is not clearly explained

Figure 6, what is the parameter on the y-axis corresponding to infection status?

Figure 7, not essential for anyone who has already seen an electrophoresis gel

The supplementary material is not “supplementary” as it is already included in the manuscript

Comments on the Quality of English Language

The text needs to be proofread by a native English speaker

Author Response

Response 1: [Thank you for pointing We agree with this comment. Therefore, regarding the analysis, the comparison with traditional cocoa planting material was done in another experimentation before this study and only the best varieties were scaling up in this pilot involving 1200 farmers. So the purpose of this experimentation was to assess the production of the promising cocoa varieties at farm level. So, we don’t need no more a traditional cocoa control.]

Comments 2: [Furthermore, the comparative results between the three technologies are not particularly surprising, given that the mature trees from infected areas were not tested for the presence of the virus prior to grafting.]

Response 2: [Secondly, we are agreeing with you on the results on mature tree grafting, but these results showed evidence with data. It is one an important lesson learnt to build on the coming initiatives on rehabilitation of CSSD infected areas in West Africa as we gave some orientations in the recommendation paragraph.]

Comments 3: [It is also somewhat risky to present results without mentioning the cocoa genotypes observed. Surprisingly, clones are only selected for their productivity, the butter quality and the resistance to black pod disease but not the tolerance to Swollen shoot. Furthermore, the hybrids are not described in any greater detail than as ‘improved coca planting material’. It would have been interesting to know their genotypes for the clones and the hybrids so as to be able to make comparisons with other publications. Just a code number is not sufficient to publish this work.]

Response 3: [Regarding the clones and hybrids used in this experimentation, the recurrent and reciprocal cocoa breeding program in Côte d'Ivoire is in its 2nd cycle of crossing Upper Amazonian Forastero (HA)2 and a mixture of Lower Amazonian Forastero and Trinitario (BA + T)2. Added in Line 110-113. This selection strategy did not consider swollen shoot disease as screening criteria until the reemergence outbreaks recorded from 2000. Also, the initial design of the vision for change project (V4C) was to address mostly rehabilitation of aged farms and improve the production through yield. The threat of swollen shoot came during the implementation phase of the V4C project. Thus, in this study we demonstrated what could be happened when the rehabilitation process did not consider the epidemiology principle of swollen shoot disease in infected landscape. The hybrids are a pool of more than 5 cocoa varieties propagated to farmers through research station and the usual name is “cacao Mercedes” due to the precocity of production.]

4. Response to Comments on the Quality of English Language

Point 1: The English could be improved to more clearly express the research

Response 1: The English has been improved as requested

5. Additional clarifications

[Here, mention any other clarifications you would like to provide to the journal editor/reviewer.]

Specific comments

The lines are not numbered, which makes it very difficult to list the corrections to be taken into account; Line number added to the manuscript.

Page 2 replace “a group of Badnavirus species” by “ a complex of Badnavirus species” Done at Line 67

Page 4: The description of the PCR mix must specify the final concentrations used for each component; simply stating the volume of a solution whose concentration is unknown is not sufficient. The PCR reaction mix of 25 µL contained 0,4 µM each of forward and reverse primer, Taq DNA polymerase (0.625 U), 1X PCR buffer, dNTPs (0.2 mM), MgCl₂ (1 mM), and 1 µg of DNA. Done at Line 200-2002

The definition given for prevalence rate and incidence rate simply refer to prevalence and incidence. These definitions should be given earlier when these terms are introduced page 3 Done and insert at Line 124-125

Page 6:

To which year of observation do the values in Table 1 correspond? 2021 Added in the title of the table in Line 259

Is there a link between the GVV plots monitored for yield (68 plots) and the plots presented in table 1 (57 plots). Yes, they are the same plots with missing data due mainly the plots are abandoned or inaccessible.

Page 7

What does mean “the required number of tree infected plots”

Figure 5B, the calculation of the severity score per clone is not clearly explained

The scale is explained in the chapter "On-farm characterization of CSSD typical infection" with scores from 1 to 6. In the calculation/graphic we initially used the scale from 1-5 and a score of 16 upon death of the plant. I adapted the graphic accordingly.
The calculation is the sum of the scores for each category.

Figure 6, what is the parameter on the y-axis corresponding to infection status?

"Observations for plots of 0,25ha"

Figure 7, not essential for anyone who has already seen an electrophoresis gel

The supplementary material is not “supplementary” as it is already included in the manuscript

Comments on the Quality of English Language

The text needs to be proofread by a native English speaker

The language has been improved as requested

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

General Comment

This manuscript investigated CSSD reinfection characteristics across three cocoa rehabilitation systems (GVV, RPG, RPH) in southwestern Côte d’Ivoire via multi-scale field monitoring combined with PCR-based latent infection detection. The topic matches the scope of Crops, focusing on viral disease epidemiology and practical improvement of crop disease management in tropical cash crop production. The experimental framework including landscape-level survey, on-farm disease assessment and molecular diagnosis is well-structured, datasets and associated figures/tables are complete, and core findings provide direct evidence to revise official CSSD tree-cutting buffer standards in West Africa cocoa-growing regions. However, substantial revisions are required on English writing, experimental description integrity, result interpretation and discussion depth before acceptance for publication.

Detailed Revision Suggestions

Abstract & Simple Summary

Remove inappropriate analogy “caused by a plant virus as Aids or Covid-19 in comparison to human case” in Simple Summary; such human disease comparison is unscientific for plant virology description.
Correct typo: virus epidemy → virus epidemic in Keywords.

3. Materials and Methods (Major revision required)

Provide detailed origin and breeding information of four tested clones (C1, C9, C15, C16) and specific commercial name of hybrid seedlings used in RPH treatment.
Explain why yield data was only collected from Q1 to Q3 instead of full-year harvest.
Improve mealybug sampling description: clarify why only stems within 0–1.5 m above ground were surveyed.

Results

Mark corresponding sampling locations for each electrophoresis lane in Figure 7 legend. The quality of Figure 7 should be enhanced.
Add brief preliminary interpretation for non-significant yield difference between symptomatic and asymptomatic GVV plots (results in table 2).

Discussion

Strengthen cross-comparison with published CSSD epidemiological data from Ghana, Togo and other West African cocoa zones, analyze climate and cropping-system-induced discrepancies in latent infection rate.
Further discuss the contribution of latent virus carried by grafted scion or residual old rootstock to central-focused infection inside GVV plots, apart from virus invasion from surrounding diseased fields.

Conclusion

Refine actionable field recommendations for local farmers and agricultural authorities.

Language, Spelling and Reference Format

Fix multiple spelling mistakes throughout manuscript: Tones → tonnes, out-breaks → outbreak.

Author Response

Comments 1: [However, substantial revisions are required on English writing, experimental description integrity, result interpretation and discussion depth before acceptance for publication]

Response 1: [English writing: Review done through the manuscript revision; Experimental description integrity: done; results interpretation and discussion: done with the work of Oro et al in Togo and Ameyaw et al in Ghana]

4. Response to Comments on the Quality of English Language

Point 1: The English could be improved to more clearly express the research

Response 1: The English has been improved as requested

5. Additional clarifications

[Here, mention any other clarifications you would like to provide to the journal editor/reviewer.]

Specific comments

Detailed Revision Suggestions

Abstract & Simple Summary

Remove inappropriate analogy “caused by a plant virus as Aids or Covid-19 in comparison to human case” in Simple Summary; such human disease comparison is unscientific for plant virology description. Done

Correct typo: virus epidemy → virus epidemic in Keywords. Done in Line 57

. Materials and Methods (Major revision required)

Provide detailed origin and breeding information of four tested clones (C1, C9, C15, C16) and specific commercial name of hybrid seedlings used in RPH treatment. The recurrent and reciprocal cocoa breeding program in Côte d'Ivoire is in its 2nd cycle of crossing Upper Amazonian Forastero (HA)2 and a mixture of Lower Amazonian Forastero and Trinitario (BA + T)2. Added in Line 110-113.

Explain why yield data was only collected from Q1 to Q3 instead of full-year harvest. The yield data were collected each year in a sample selected sites of the 1200 farms until the Q3 of 2021. We used Q1-Q3 data in this paper because in this period, the field investigation for CSSD statute was effectively conducted in the farms where yield data were recorded.

Improve mealybug sampling description: clarify why only stems within 0–1.5 m above ground was surveyed. It’s one of the methods for mealybugs observation in cocoa field. The mealybugs are mostly on cocoa pods on trunk and 1.5 m corresponding to an area where the field staff can easily observe this part of the tree by counting and identifying the different insects in presence. Added in line 176-178.

Results

Mark corresponding sampling locations for each electrophoresis lane in Figure 7 legend. The quality of Figure 7 should be enhanced.
Add brief preliminary interpretation for non-significant yield difference between symptomatic and asymptomatic GVV plots (results in table 2). This result indicated that the initial phase of CSSD infection, the yield decreasing was not perceptible, and the infected trees continued producing normally until the virus load reach a threshold. In Line 272-274

Discussion

Strengthen cross-comparison with published CSSD epidemiological data from Ghana, Togo and other West African cocoa zones, analyze climate and cropping-system-induced discrepancies in latent infection rate.

Done with the work of Oro et al in Togo and Ameyaw et al in Ghana. Line 405-408

Further discuss the contribution of latent virus carried by grafted scion or residual old rootstock to central-focused infection inside GVV plots, apart from virus invasion from surrounding diseased fields. Done Line Added Line 415-418

Conclusion

Refine actionable field recommendations for local farmers and agricultural authorities. Done Line 498-506

Language, Spelling and Reference Format

Fix multiple spelling mistakes throughout manuscript: Tones → tonnes, out-breaks → outbreak. The language has been improved in the whole manuscript as requested.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

This study investigated appearance and distribution of cocoa swollen shoot disease (CSSD) on rehabilitated farms in south-western Côte d'Ivoire. Results indicated that the disease could reappear more rapidly than expected in specifics conditions linked with cultural practices, resistance of planting materials and the awareness of farmers. Lessons learnt from this study are important to an integrated management of the disease and an efficient protection of young, replanted farms. In general, the experiments were well-performed.

1) All abbreviations should be introduced with full names, for examples AIDS and COVID-19 in Abstract, GVV, RPG and RPH in Table 1.

2) And the Abstract should be re-written. No any value or number is shown in the Abstract, which is unacceptable.

3) In Table 1, the p value for each column should be shown.

4) What are Q1 and Q3 in Table 2?

5) What is "Limit of the nearest CSSD outbreak to pilot plot"? And what are State 1 and State 2?

6) In Figures 4 and 5, the error bars are large to be true. But the letters in these figures are too small to be seen clearly.

7) I cannot understand Figure 8. More description is needed in the legend.

Comments on the Quality of English Language

The language is poor and should be polished by an English native speaker.

For instances in Abstract:

A plant disease should not be compared with human infectious diseases.

"the evolution of the disease" was not studied in this report.

"based on removal all infected areas and replanted using best agricultural practices" How to remove areas?! What are the best agricultural practices?

"...linked the cultural practices, the resistance of the planting material and the awareness of the farmers" So many words "the" in this sentence!

"disease could reappear more rapidly than expected" What was the expected value? How to define rapid or slow?

"replanted farms after treated the infection areas" after treatments to the infected areas? What treatments?

What is the "landscape level"?

Author Response

Comments 1: [However, the analyses carried out are not particularly convincing, as they lack comparisons with unimproved control genotypes. The incidence of the disease probably depends as much on the genotypes used and, above all, on the proximity of infected plots as it does on the rehabilitation technology. Furthermore, the comparative results between the three technologies are not particularly surprising, given that the mature trees from infected areas were not tested for the presence of the virus prior to grafting.]

Response 1: [Thank you for pointing We agree with this comment. Therefore, regarding the analysis, the comparison with traditional cocoa planting material was done in another experimentation before this study and only the best varieties were scaling up in this pilot involving 1200 farmers. So, the purpose of this experimentation was to assess the production of the promising cocoa varieties at farm level. So, we don’t need no more a traditional cocoa control.]

Comments 2: [It is also somewhat risky to present results without mentioning the cocoa genotypes observed. Surprisingly, clones are only selected for their productivity, the butter quality and the resistance to black pod disease but not the tolerance to Swollen shoot. Furthermore, the hybrids are not described in any greater detail than as ‘improved coca planting material’. It would have been interesting to know their genotypes for the clones and the hybrids so as to be able to make comparisons with other publications. Just a code number is not sufficient to publish this work..]

Response 2: [the recurrent and reciprocal cocoa breeding program in Côte d'Ivoire is in its 2nd cycle of crossing Upper Amazonian Forastero (HA)2 and a mixture of Lower Amazonian Forastero and Trinitario (BA + T)2. Added in Line 110-113. This selection strategy did not consider swollen shoot disease as screening criteria until the reemergence outbreaks recorded from 2000.]

4. Response to Comments on the Quality of English Language

Point 1: The English could be improved to more clearly express the research

Response 1: As requested, the English has been improved in all the paragraph of the manuscript

5. Additional clarifications

[.]

Comments and Suggestions for Authors

1) All abbreviations should be introduced with full names, for examples AIDS and COVID-19 in Abstract, GVV, RPG and RPH in Table 1.Done

2) And the Abstract should be re-written. No any value or number is shown in the Abstract, which is unacceptable. Done

3) In Table 1, the p value for each column should be shown.

4) What are Q1 and Q3 in Table 2? Q1= Quarter 1 and Q3= Quarter 3. The yield data were collected each year in a sample selected sites of the 1200 farms until the Q3 of 2021. We used Q1-Q3 data in this paper because in this period, the field investigation for CSSD statute was effectively conducted in the farms where yield data were recorded.

5) What is "Limit of the nearest CSSD outbreak to pilot plot"? And what are State 1 and State 2? Cocoa farms are established in a continuous large band /space with virtual limit in Soubre area in Côte d’Ivoire. Only the select farms in the soubre cocoa landscape for the pilot have been treated as described in this methodology and the nearest CSSD outbreaks corresponding to the neighbor intreated farms and presenting visible CSSD symptoms/outbreaks.

6) In Figures 4 and 5, the error bars are large to be true. But the letters in these figures are too small to be seen clearly.

Figure 5 B. The whiskers where indeed wrong because of a higher score for dead plants (16). The boxplot has been adapted. The boxplots for figure 4 and 5 show the following values:

Box: Encompasses the interquartile range (IQR) = 25%–75% of the data
Line inside the box: Median (50th percentile, middle value)
Upper edge of the box: 3rd Quartile (Q3) = 75% of values are below this
Lower edge of the box: 1st Quartile (Q1) = 25% of values are below this
Upper "whisker" (line above): Maximum within 1.5×IQR from Q3
Lower "whisker" (line below): Minimum within 1.5×IQR from Q1
Circles (o): Outliers = values between 1.5× and 3×IQR from the box edge

Figure 5 A + B the police size has been adapted

7) I cannot understand Figure 8. More description is needed in the legend. Done

Comments on the Quality of English Language

The language is poor and should be polished by an English native speaker. The language has been improved in the whole manuscript as requested.

For instances in Abstract:

A plant disease should not be compared with human infectious diseases.

"the evolution of the disease" was not studied in this report.

"based on removal all infected areas and replanted using best agricultural practices" How to remove areas?! What are the best agricultural practices?

"...linked the cultural practices, the resistance of the planting material and the awareness of the farmers" So many words "the" in this sentence!

"disease could reappear more rapidly than expected" What was the expected value? How to define rapid or slow?

"replanted farms after treated the infection areas" after treatments to the infected areas? What treatments?

What is the "landscape level"?

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

There are still many inaccuracies and uncorrected errors.
For example, the authors state in “Response 3” that they have corrected the description of the genetic crosses used to create hybrids 110–113, but this is not the case. The definition of the incidence rate lines 104-105 is only the definition of incidence, note incidence rate. I believe it is necessary to provide information on the genotypes used in these trials.

Furthermore, the conclusions of this publication are valid but not really relevant to the results produced.

I do not wish to proofread a manuscript that was apparently submitted the first time without being proofread by the other authors – given the number of errors – and which, on this second occasion, has not been proofread thoroughly enough either.

Author Response

Comments 1: [There are still many inaccuracies and uncorrected errors.

For example, the authors state in “Response 3” that they have corrected the description of the genetic crosses used to create hybrids 110–113, but this is not the case.]

Response 1: [The genetic crosses used to create clones and hybrids is confidential since the beginning of the V4C project in Côte d’Ivoire and could not be shared in this paper, but we clearly indicated the references papers on the general ongoing cocoa breeding in Côte d’Ivoire.] L93-102

Comments 2: [The definition of the incidence rate lines 104-105 is only the definition of incidence, note incidence rate.]

Response 2: [Done L105-L1017.]

Comments 3: [I believe it is necessary to provide information on the genotypes used in these trials]

Response 3: [The genetic crosses used to create clones and hybrids is confidential since the beginning of the V4C project in Côte d’Ivoire and could not be shared in this paper, but we clearly indicated the references papers on the general ongoing cocoa breeding in Côte d’Ivoire.]

Comments 4: [I do not wish to proofread a manuscript that was apparently submitted the first time without being proofread by the other authors – given the number of errors – and which, on this second occasion, has not been proofread thoroughly enough either.]

Response 3: [This is your point of view. We are respectful on that, and we don’t want to comment. ALL the authors have approved and read this manuscript ]

4. Response to Comments on the Quality of English Language

Point 1: The English could be improved to more clearly express the research

Response 1: The English has been improved two time during this review process as requested by 2 native English and scientific men.

5. Additional clarifications

E[Here, mention any other clarifications you would like to provide to the journal editor/reviewer.]

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors The manuscript has undergone sufficient revisions and meets the publication standards of this journal. No further revisions are required.

Author Response

Comments 1: The manuscript has undergone sufficient revisions and meets the publication standards of this journal. No further revisions are required.]

Response 1: [Thanks you]

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

In general, I'm satisfied with the revision. However, the numbers and the letters in Figure 8 are too small to be seen clearly.

Author Response

Comments 1: [In general, I'm satisfied with the revision. However, the numbers and the letters in Figure 8 are too small to be seen clearly.]

Response 1: [The number and the letters in figure 8 have been improved. Thank you]

Author Response File: Author Response.pdf