Dear Dr. Raza,

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Kind regards,

Md. Kamrujjaman, Ph.D

Academic Editor

PLOS ONE

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Reviewer's Responses to Questions

Comments to the Author

1. Is the manuscript technically sound, and do the data support the conclusions?

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Partly

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2. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: No

Reviewer #2: I Don't Know

Reviewer #3: Yes

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3. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: No

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4. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: No

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: The authors should rewrite the manuscript to address all noted concerns, verify all mathematical derivations and results, and resubmit only after thorough revision. Even I am not sure whether it's possible to overcome, especially the theoretical analysis. Due to the pervasive issues in clarity, mathematical correctness, and presentation, the manuscript requires substantial revision.

Reviewer #2: This manuscript presents a comprehensive and mathematically rigorous analysis of a stochastic delayed differential equation model for Maize Streak Virus (MSV) dynamics. The work is well-structured, moving from a deterministic formulation to a complex stochastic model with time delays. The analytical proofs for positivity, boundedness, equilibrium stability, and disease extinction are thorough.

A significant strength of the paper is the detailed comparison of various stochastic numerical methods (Euler-Maruyama, Runge-Kutta, NSFD), with a clear demonstration of the advantages of the stochastic Non-Standard Finite Difference (NSFD) scheme in terms of stability and step-size independence. The discussion on the impact of time delay (τ) on the basic reproduction number (R₀) and disease dynamics is particularly insightful and valuable for understanding control strategies. The manuscript is suitable for publication in PLOS ONE after the authors address the following points, which primarily aim to clarify methodology and strengthen the discussion.

1. Model Parameterization and Validation: The parameters in Table 2 are listed as "Fitted" or "Estimated." Could you please provide more detail on the data source and the procedure used for this parameter estimation or fitting? Furthermore, how were the values for the stochastic noise intensities (σ₁ to σ₅) chosen for the simulations in Section 8?

2, Clarification of Stochastic Formulations: The manuscript presents two different stochastic formulations (Phase 1 in Eqs. 9-10 and Phase 2 in Eqs. 11-15). Phase 1 uses a complex diffusion matrix derived from transition probabilities, while Phase 2 uses a simpler, more common linear multiplicative noise. Could you clarify the relationship between these two approaches and justify why the analysis and numerical simulations primarily focus on the model from Phase 2?

3. "Bioinformatics" in the Title and Scope: The term "Bioinformatics" is prominently featured in the title, yet the manuscript is predominantly a mathematical and computational modeling study. Could you elaborate on the specific bioinformatics analyses performed (e.g., sequence data analysis, phylogenetic analysis) or clarify the usage of the term to align better with the paper's core content, perhaps focusing on "computational biology"?

4. Numerical Comparison Metrics: The conclusion states that the stochastic NSFD approach is the "most accurate, productive, and efficient." To strengthen this claim, could you provide quantitative metrics for this comparison, such as computational time (CPU time), mean squared error compared to a benchmark solution, or stability region analyses for the different methods?

5. Biological Interpretation of Delay (τ): The time delay τ is a critical component of the model. While its mathematical impact is well-demonstrated, could you provide a more detailed biological interpretation? What specific biological processes (e.g., the latent period in the insect vector, the incubation period within the plant, or a delay in implementing control measures) is this delay intended to represent?

6. Impact of Insecticide Treatment: The parameter γ represents the efficacy of the insecticide treatment. The analysis shows its role in the reproduction number R₀, but could you discuss the simulation results that specifically illustrate the impact of varying γ on the infected plant population? This would provide direct insights into the effectiveness of insecticide-based control strategies.

Suggested References for Inclusion

The authors are also requested to consider citing the following recent papers, which demonstrate advanced numerical techniques for solving fractional and stochastic differential equations. These references would provide a broader context for the computational methods used in this manuscript and highlight the applicability of such schemes in complex modeling scenarios.

For advanced collocation methods:

1. Raza, A., et al. "Collocation method with Morgan-Voyce polynomials to solve the time fractional long memory Black-Scholes model with jump process." Scientific Reports (2024). This work showcases a high-precision numerical technique for financial models with memory and jumps, which is methodologically relevant to the stochastic schemes discussed here.

For enhanced numerical solutions of fractional dynamics:

2. Raza, A., et al. "Enhanced numerical solution for time fractional Kuramoto–Sivashinsky dynamics via shifted companion Morgan–Voyce polynomials." Scientific Reports (2024). This paper presents an efficient spectral method for nonlinear fractional PDEs, underscoring the importance of robust numerical solvers in computational biology and other fields.

Reviewer #3: Please take a look at the attached detailed review document for full comments and recommendations. I have addressed each evaluation point thoroughly in the attached file. Going through those points will be enough.

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what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes:  Nuzhat Nuari Khan Rivu

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Attachments

Attachment

Submitted filename: Review comment.pdf

Attachment

Submitted filename: review.pdf

Computational Analysis of Stochastic Delay Dynamics in Maize Streak Virus

PONE-D-25-54354R1

Dear Dr. Raza,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Md. Kamrujjaman, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

Reviewer #3: All comments have been addressed

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2. Is the manuscript technically sound, and do the data support the conclusions??>

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously? -->?>

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available??>

The PLOS Data policy

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: No

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5. Is the manuscript presented in an intelligible fashion and written in standard English??>

Reviewer #1: Yes

Reviewer #2: Yes

Reviewer #3: Yes

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Reviewer #1: After a thorough evaluation of the revised manuscript, I am satisfied that the authors have carefully and comprehensively addressed all the comments and suggestions raised during the initial round of review. The revisions have significantly improved the clarity, organization, and scientific rigor of the manuscript.

All methodological issues have been appropriately clarified, the presentation of results has been enhanced, and the discussion has been strengthened to reflect the study’s contributions more effectively. The manuscript now demonstrates coherence, proper referencing, and adherence to the journal’s formatting and academic standards.

Given that the authors have fulfilled all the review criteria and the manuscript now meets the required quality for scholarly publication, I am pleased to recommend it for publication.

Reviewer #2: (No Response)

Reviewer #3: The revised manuscript addresses previous comments effectively, and the technical presentation is now clear and well-organized. Everything appears satisfactory. However, I recommend that the authors make their simulation codes publicly available (for example, by uploading them to a GitHub repository). This will enhance transparency and allow other researchers to reproduce or extend the study in the future.

**********

what does this mean? ). If published, this will include your full peer review and any attached files.

If you choose “no”, your identity will remain anonymous but your review may still be made public.

Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy

Reviewer #1: No

Reviewer #2: No

Reviewer #3: Yes:  Nuzhat Nuari Khan Rivu

**********

Attachments

Attachment

Submitted filename: R2_Review comment.pdf