Phylogenetic and Genetic Variation Analysis of Porcine Epidemic Diarrhea Virus in East Central China during 2020–2023
, Duo Li 1,2, Caijie Yan 1,2, Chengyue Wu 1,2, Feng Han 1,2, Zongyi Bo 3,4, Manman Shen 1,2, Yiwei Sun 1,2, Liyan Wang 1,2, Haoqin Zheng 1,2, Mengdong Wang 1,2 and Zhendong Zhang 1,2,3,4,*
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.
