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Authors have addressed my comments.
[# PeerJ Staff Note - this decision was reviewed and approved by Fanglin Guan, a PeerJ Section Editor covering this Section #]
For the odds ratios (ORs) presented in the tables, the authors should define a reference category with an OR set to 1 and calculate the remaining ORs accordingly. It is important to maintain consistency in the choice of reference genotype throughout the article. As currently presented in Table 4, the results appear inadequate, since the p-values will remain the same and the ORs will be reciprocal values (i.e., 1 divided by the other OR).
Some sentences are still awkward or unclear to English readers. For example:
- Line 143: “Acquired immunity was still the main pathway against viruses” — does this imply it no longer is? Please clarify.
- Line 163: “RNA structure was important to regulatory fate and function of encoding protein” — does this refer to past relevance only? Consider rephrasing for clarity.
Please revise the manuscript for improved language and clarity.
One additional suggestion for future manuscripts: avoid using the Kolmogorov-Smirnov test to assess normality. Its low statistical power has been well-documented since the 1980s (e.g., 10.1186/s13742-015-0048-7). To quote a seminal reference:
“... for testing for normality, the Kolmogorov-Smirnov test is only a historical curiosity. It should never be used. It has poor power in comparison to specialized tests such as Shapiro-Wilk, D’Agostino-Pearson, Bowman-Shenton, and Anderson-Darling tests.”
— D’Agostino, R.B. and Stephens, M.A. (1986). Goodness-of-Fit Techniques. New York: Marcel Dekker.
No comment.
No comment.
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Please see the reviewers' comments below and respond in detail
• The English is good and require just a few adjusts to improve concordance. (Ex: These results suggested that genetic variants of the SHFL gene was associated with HCV).
• The text is well written, clear, and objective.
• The authors provided sufficient literature references.
• The methodology could be improved just adding the test used to evaluate normality of continuous data on Data Analysis section.
The “Genetic variations of the SHFL gene associated with HCV infection in Yunnan population” is a Research Article. It focuses on 3 variants of SHFL (C19orf66) gene —rs77076061-T/A, rs1979262-A/G, and rs12611087-T/C— and their possible role on Hepatitis C infection. The polymorphisms alter the intronic portion that originates the SHFL RNA, which possibly influence on its function on people infected by HCV. One of the main founds is that heterozygous genotypes of these variants were risk factors for HCV infection in Yunnan population.
The authors presented that variants of SHFL gene could alter the protein and consequently probably would affect its function and the HCV infection. However, your manuscript could be improved with some adjusts:
• The results of rs12611087 variant are kind confuse on Table 1 because every result was meaningful (p<0.05). Have you done any comparison using dominant or recessive model? If not, please emphasize on your text which genotype is more beneficial for HCV infected people.
• In the sentence “Together with Kinast s report, we indicated that the SHFL gene could inhibit HCV replication by both genetic and functional aspects” you could switch the “inhibit” verb for “affect”.
That is because in the present study there is not any specific essay to evaluate viral replication (e.g., plating assays, RT-qPCR after infecting cells with HCV) and there was not any significant difference on viral load of patients with different variants of SHFL.
Background
• Maybe you should consider do a brief comment about the 3 variants you chose for your study, such as its prevalence in EAS region.
Material and Methods
Subjects section
• Do “Not co-infected with Hepatitis B virus (HBV) and/ or HIV” was the only exclusion criteria? Which other characteristics were used? Did any other clinical manifestation which could affect hepatitis C outcomes (e.g.: comorbidities) were evaluated?
In this manuscript 347 HCV patients and 448 general controls were evaluated concerning three SNPs in the SHFL gene. The present manuscript has major issues that should be addressed by the authors:
The main question is that the results of the control group are duplicated from a previously study by Liu et al. 2023, which evaluated these same polymorphic variants and susceptibility to HBV infection in this same human population. Also, the same data was again published (on PeerJ, actually) as controls for a comparison with HIV positive patients (see Zhang et al. 2023). Authors should refer to previously published data.
The manuscript will benefit from an extensive review of the English-language usage and grammar.
Several sentences should be revised. For example:
a. in the sentence “Parts of HCV infection could not be immediately recognized by immune system of host, and further develop into chronic HCV infection.” the term “parts of HCV infection” could be misleading, as could also be misleading the idea of an “immediate recognition by the immune system”.
b. instead of saying “…and their genetic variants were widely associated with HCV infection or treatment effect”, I would suggest to add that “… some of their genetic variants …”
c. avoid the use of “and so forth”. It is better to add and cite the relevant information.
Besides, there are several misleading concepts. The usage of the term "allele", for example, should be revised along the manuscript.
Please, explain the following sentence in the Discussion “Together with Kinasts report, we indicated that the SHFL gene could inhibit HCV replication by both genetic and functional aspects.”
I would recommend a review of the statistics by an expert, since I was not able to found the same numbers as the authors.
Although a potential involvement of the SHFL gene expression and HCV infection is supported by the literature, authors should better justify the choice of this specific gene variants.
Finally, the results concerning the RNA structure prediction of the three SNPs, as well as the discussion approaching these results are quite shallow and deserve to be better explored.
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