Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThis paper enriches our understanding of the epidemiology of PEDV in Jiangsu and Anhui provinces of CHINA.Here are the specific comments:
1 Line 53 and Line 56, there are levant symbol present within the word of “pro-tein” and “adsorp-tion”.Please check the whole article carefully.
2 Part 2.1 requires a description of the number and area of distribution of the clinical samples.
3 Part 2.2,this paper doesn't seem to use Restriction Endonuclease.If it is necessary, please specify which one?
4 The authors used test primers for screening, but there were no screening results.
5 Whether it is necessary to state that the nine sequences originate from different pig farms?
6 Previous studies identified multiple neutralizingepitopes,I suggest that the authors compare all neutralizingepitopes mutations.
Author Response
Overall Statement: This paper enriches our understanding of the epidemiology of PEDV in Jiangsu and Anhui provinces of CHINA. Here are the specific comments:
Comment #1: Line 53 and Line 56, there are levant symbol present within the word of “pro-tein” and “adsorp-tion”.Please check the whole article carefully.
Response: We deeply appreciated the reviewer’s helpful suggestion. The levant symbol present within the word of “pro-tein” and “adsorp-tion” already be removed from these words, and we checked the whole article to avoid this mistake. (Please refer to line 36-38, 47,50,59,268-269, 296,302,306)
Comment #2: Part 2.1 requires a description of the number and area of distribution of the clinical samples.
Response: We deeply appreciated the reviewer’s insightful suggestion and have made a description of the number and area of distribution of the clinical samples. (Please refer to line 71-79)
Comment #3: Part 2.2,this paper doesn't seem to use Restriction Endonuclease.If it is necessary, please specify which one?
Response: Thanks for your helpful suggestion. We are so sorry for that errors, we didn’t use Restriction Endonuclease. We modified this information. (Please refer to line 89-102)
Comment #4: The authors used test primers for screening, but there were no screening results.
Response: Thanks for your helpful suggestion. We added the description of RT-PCR results in line 121-123.
Comment #5: Whether it is necessary to state that the nine sequences originate from different pig farms?
Response: We deeply appreciated the reviewer’s helpful suggestion. we stated that it in line 135-136.
Comment #6: Previous studies identified multiple neutralizingepitopes,I suggest that the authors compare all neutralizingepitopes mutations.
Response: We deeply appreciated the reviewer’s helpful suggestion. We compared all neutralizing epitopes mutations including COE (499-638aa), SS2 (748–755 aa), SS6 (764–771 aa) and 2C10 (1368–1374 aa). And We described the results in line 204-208.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript basically gains the following 3 points:
1. the emergence of 3 variants during 2020-2023.
2. These 3 variants likely derived from recombination of parental (backbone) variants with a donor variants.
3. There are novel mutations on amino acid 141-148 in the 9 analyzed variants.
Therefore, the simple summary and abstract should be rewritten. They can be shortened extensively.
line 70: fecal samples were collected from normal piglets, so what you are characterizing here may be non-pathogenic variants. It would be more significant to sample from diarrhea piglets and correlated the disease with antigenicity change.
line 94: the "mutation" is incorrect. What you tried to avoid is "replication error" by the amplifying enzyme.
Sections 2.2, 2.4 and 2.5 should be combined into one section.
Table 3: mark, on the first column, the three G1c subgroup variants.
line 165: "distant from" is an alternative for "far related".
section 3.3: the recombinants have 3 major fragments, discuss how many cross-over (2? or at least 2) does it take to get such recombinants.
Figure 4: mark, on this figure, where is the patch of amino acids coded by the acquired "710-1190 bp" (line 182). It should be present on 3 variants.
Figure 5: it is better to have three-dimension (3-D) modeling of the S protein in order to show that this 141-149 aa are actually located or exposed at the key surface for antigenicity.
line 244: discuss how many cross-over (2? or at least 2) does it take to get such recombinant.
Author Response
The manuscript basically gains the following 3 points:
- the emergence of 3 variants during 2020-2023.
- These 3 variants likely derived from recombination of parental (backbone) variants with a donor variants.
- There are novel mutations on amino acid 141-148 in the 9 analyzed variants.
Comment #1: Therefore, the simple summary and abstract should be rewritten. They can be shortened extensively.
Response: We deeply appreciated the reviewer’s helpful suggestion. The simple summary and abstract were rewritten.
Comment #2: line 70: fecal samples were collected from normal piglets, so what you are characterizing here may be non-pathogenic variants. It would be more significant to sample from diarrhea piglets and correlated the disease with antigenicity change.
Response: We deeply appreciated the reviewer’s helpful suggestion. Our fecal samples were collected from diseased piglets with diarrheic symptoms. we added this information in line 64, 73-75.
Comment #3: line 94: the "mutation" is incorrect. What you tried to avoid is "replication error" by the amplifying enzyme.
Response: Thanks for your helpful suggestion, the word was changed into " replication error " accordingly. (Please refer to line 84)
Comment #4: Sections 2.2, 2.4 and 2.5 should be combined into one section.
Response: We deeply appreciated the reviewer’s helpful suggestion. As suggested, sections 2.2, 2.4 and 2.5 already be combined into one section. (Please refer to line 88-102)
Comment #5: Table 3: mark, on the first column, the three G1c subgroup variants.
Response: Thanks for your helpful suggestion, we marked the subgroup of variants on the first column in Table 3. (Please refer to line 148-149)
Comment #6: line 165: "distant from" is an alternative for "far related".
Response: Thanks for your helpful suggestion, the word was changed into " distant from " accordingly. (Please refer to line 160)
Comment #7: section 3.3: the recombinants have 3 major fragments, discuss how many cross-over (2? or at least 2) does it take to get such recombinants.
Response: Thanks for your helpful suggestion, we discuss that in line 179-185. (Please refer to line 160)
Comment #8: Figure 4: mark, on this figure, where is the patch of amino acids coded by the acquired "710-1190 bp" (line 182). It should be present on 3 variants.
Response: Thanks for your helpful suggestion, the patch of amino acids coded by the acquired "710-1190 bp" was present on 3 variants. (Please refer to line 215-216)
Comment #9: Figure 5: it is better to have three-dimension (3-D) modeling of the S protein in order to show that this 141-149 aa are actually located or exposed at the key surface for antigenicity.
Response: We deeply appreciated the reviewer’s helpful suggestion. As suggested, hree-dimension (3-D) modeling of the S protein of 3 variants were shown in Figure 5. And we added the description the results in text. (Please refer to line 232-241)
Comment #10: line 244: discuss how many cross-over (2? or at least 2) does it take to get such recombinant.
Response: We deeply appreciated the reviewer’s helpful suggestion. We discussed that in line 263-268 (Please refer to line 263-268)
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe R1 of version of this manuscript has improved. All my concerns have been addressed.