PONE-D-20-23288

The Genotype Distribution, Infection Stage and Drug Resistance Mutation Profile of Human Immunodeficiency Virus-1 among the Infected Blood Donors from Five Chinese Blood Centers, 2014-2017

PLOS ONE

Dear Dr. He,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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We look forward to receiving your revised manuscript.

Kind regards,

Chiyu Zhang, Ph.D.

Academic Editor

PLOS ONE

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'Human Subject Research

name：Chinese Academy of Medical sciences/Peking Union Medical College ethical reriew committee

the approval number:X101222002

form:written'

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4. Please amend the manuscript submission data (via Edit Submission) to include authors Liu Zhiyang, Wang Shaoli, Liu Jing, Shi Ling, Mao Wei, Liu Cunxu, Wan Jianhua, Zhu Lili, Huang Mei, Liu Yu, Wang Jingxing, Paul Ness, Shan Hua and Zeng Peibin.

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Reviewers' comments:

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Comments to the Author

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

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Partly

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

Reviewer #1: Yes

Reviewer #2: Yes

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

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No

Reviewer #2: Yes

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

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: No

Reviewer #2: Yes

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5. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: In this paper, the authors investigated the genotype distribution and drug resistance mutation profile of HIV-1 among HIV-1 positive patients in 5 different Chinese blood centers during July 1, 2014 - January 30, 2017. They obtained HIV-1 Pol sequences, subtyped them and analyzed the DRMs. These findings will be helpful for the prevention and control of HIV/AIDS in China.

Comments:

1)Materials and methods: The parameters for the phylogenetic analysis should be provided. The Genbank Accession Numbers of all obtained sequences should be provided. .

2)The authors mentioned that “Statistical analysis was performed using the chi-square test (or the Fisher's exact test) ” When the Fisher's exact test were used? In addition, “double-tailed test” should be “two-tailed test”..

3)Page 10, Line 184-189: The authors should carefully check the classification of DRM. for example, M184L belongs to NRTI, rather than NNRTI. “184M” should be written in a complete form.

4)Page 12, Lines 239: Reference 26 did not support the statement that “The study also points out that these new CRFS are all from MSM and spread across regions through MSM groups”.

5)Page 12, Lines 246: How the DR prevalence rate ere (12.8%, 20/156) to be calculated?

6)Page 12, Lines 249: The national HIV-1 drug resistance prevalence should be updated. Please see and cite the most recent Meta-analysis paper in EClinicalMedicine. 2020 Jan 5;18:100238.

7)Page 13, Lines 264: The statement that “the V179E may be transmitted” should be supported by phylogenetic analysis.

8)The detailed demographic characteristics (age, gender, education, occupation and so on), subtypes, and DRMs of recruited patients should be provided.

9)S1 Table: Wrong classification of DRMs and incomplete drug sensitivity of patients.

10)Language can be further improved.

Reviewer #2: Comments to the Author:

This paper reports characteristics of HIV-1 subtype distribution, infection stages and drug resistance among blood donors from five Chinese blood centers (Chongqing, Guangxi, Luoyang, Mianyang and Urumqi) in 2014-2017. However, the HIV-1 subtype data shown in Table 1 and Figure 2 are not consistent. So the results of the article seem unconvincing. A re-analysis of HIV-1 subtype data are suggested. Thus, my suggestion is the manuscript needs major revisions before it can be published. The following comments may be helpful for the revision of this paper.

Major comments:

1. The HIV-1 subtype data shown in Table 1 and Figure 2 are not consistent. In Table 1 and Figure 2, the total number of Subtypes B, CRF69_01B and CRF62_BC were 15 and 17, respectively. Sequence CRF69_01B from Chongqing unmarked the color of node. The caption of CRF62_BC only including the reference sequences CRF62_BC, not the CRF62_BC sequence from Chongqing. In the subtree of CRF08_BC, CRF08_BC sequence from Urumqi unmarked the color of node. In the subtree of CRF55_01B, a total of 12 CRF55_01B sequences, however, only 11 CRF55_01B sequences showed in Table 1. In the subtree of CRF01_AE, one sequence belongs to CRF59_01B, however, no CRF59_01B appeared in the manuscript. In Table 1 and Figure 2, the number of CRF07_BC distribution in Mianyang and Guangxi were 16, 13 and 17, 11, respectively. There are two CRF_07 BC reference sequences not marked with node symbols. Please check the data carefully.

2. In recent years, HIV-1 CRF55_01B has increased from the MSM population in China. In the present study, CRF55_01B was identified among blood donors in Chongqing (n=3), Urumqi (n=4), Luoyang (n=3) and Mianyang (n=1) (Table 1). I wonder there is the transmission link between the blood donors and MSMs, or link to CRF55_01B sequences from these regions and other region in China. So, I suggest authors try to perform a Bayesian analysis to infer the original time and transmission dynamics of the CRF55_01B of these blood donors, and elucidate their migration from these different regions in China or transmission between these two populations (blood donors and MSMs).

Minor comments:

1. Line 49: As the authors mentioned, “two PIs major DRMs (M46I)”, however, the PIs major DRMs shown in Table S1 is M46I/L. The authors should check this data.

2. Line 50, Line 181: “thirty-four” should be “34”.

3. Line52-53:CRF62_BC is identified from the 01B subtype? If so, the subtype information should be checked.

4. Line 66:“sub genotypes”should be “subtypes”or “genotypes”.

5. Line 84-89: The font of the paragraph needs to be reformatted, so that the paragraph format is consistent.

6. Line 118-119, Figure 2: The HIV-1 reference sequences of CRF55_01B, CRF62_BC, CRF65_cpx, CRF68_01B and CRF69_01B is displayed the name of isolate, not the Genbank Accession Number. There are only one reference sequence for CRF55_01B, CRF62_BC, CRF65_cpx, CRF68_01B and CRF69_01B in the text, however, at least 3 reference sequences for each CRF in Figure2. Please clarify these questions.

7. Line 182, Line 254: “359” should be “358”.

8. Line 217: The font of the gene is recommended in italics, such as: pol.

9. Line 230, Line 247-250, Line 253: Place names and countries in English should be capitalized.

10. Is there a different HIV-1 drug resistance prevalence among recent infection and long-term infection? Please discuss the differences among them.

11. Figure 2: Bootstrap support value should be shown in the phylogenetic tree.

12. The format of references should be checked thoroughly.

13. Check English/grammar throughout.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-23288R1

The Genotype Distribution, Infection Stage and Drug Resistance Mutation Profile of Human Immunodeficiency Virus-1 among the Infected Blood Donors from Five Chinese Blood Centers, 2014-2017

PLOS ONE

Dear Dr. He,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Please submit your revised manuscript by Dec 20 2020 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org. When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.

Please include the following items when submitting your revised manuscript:

• A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). You should upload this letter as a separate file labeled 'Response to Reviewers'.
• A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
• An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols

We look forward to receiving your revised manuscript.

Kind regards,

Chiyu Zhang, Ph.D.

Academic Editor

PLOS ONE

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Reviewers' comments:

Reviewer's Responses to Questions

Comments to the Author

1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation.

Reviewer #1: All comments have been addressed

Reviewer #2: All comments have been addressed

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

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

**********

6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: The authors have addressed my comments and only a few minor changes to the manuscript are needed.

Minor comments:

1. This article needs to provide GenBank accession number of 356 obtained sequences.

2. Line 62: “CRF_08BC” should be “CRF08_BC”.

3. Line 113-114: “JP.AB845344_K231, JP.AB845345_K320; CRF62_BC: KC870035.1, KC870034.1, KC870037.1” should be “AB845344, AB845345; CRF62_BC: KC870035, KC870034, KC870037”.

4. Table 1: The sample size of CRF59_01B among five blood centers should be in regular font instead of bold.

5. Table 2: the total number of subtype B for recent infection should be “4”; the total number of subtype CRF01_AE for long-term infection should be “54”.

6. The sentence of line 201 should be further improved.

7. Line 218-220: The sentence (Finding substantial cases of these four CRFs) seems not accurate because the numbers of CRF55_01B, CRF59_01B and CRF68_01B were 15, 1, and 1, respectively. In addition, “four CRFs” should be “three CRFs”.

8. Line 228: “12.1% (12.1%, 43/356)” should be “12.1% (43/356)”.

9. Table 3: “250” should be “251”. “312” should be “313”. “355” should be “356”. The “P value” should be re-calculated.

10. The sentence of line 253-256 should be further improved.

11. Line 319: “A” should be “a”.

12. The format of references 8, 53, 54, 55 and 56 should be checked.

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7. PLOS authors have the option to publish the peer review history of their article (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

[NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.]

While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/. PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org. Please note that Supporting Information files do not need this step.

The Genotype Distribution, Infection Stage and Drug Resistance Mutation Profile of Human Immunodeficiency Virus-1 among the Infected Blood Donors from Five Chinese Blood Centers, 2014-2017

PONE-D-20-23288R2

Dear Dr. He,

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.

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Kind regards,

Chiyu Zhang, Ph.D.

Academic Editor

PLOS ONE

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