The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia

Indah K. Murni; Vicka Oktaria; Amanda Handley; David T. McCarthy; Celeste M. Donato; Titik Nuryastuti; Endah Supriyati; Dwi Astuti Dharma Putri; Hendri Marinda Sari; Ida Safitri Laksono; Jarir At Thobari; Julie E. Bines

doi:10.1371/journal.pone.0274793

Peer Review History

Original SubmissionMay 23, 2022
1 Jul 2022 Decision Letter - Etsuro Ito, Editor PONE-D-22-14874The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in IndonesiaPLOS ONE Dear Dr. Murni, 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. As pointed out by one of the reviewers, please describe the data of qPCR. Please submit your revised manuscript by Aug 15 2022 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. 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Reviewer #1: Yes Reviewer #2: No ****** 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: Yes Reviewer #2: No ****** 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: Yes Reviewer #2: Yes ****** 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: This paper presents a feasibility study of using wastewater-based epidemiology for early detection of SARS-CoV-2 in low- and middle in come countries. The study is based on 10-week period data collected from key locations. The results show the highest rate of 77% and the lowest rate of 25% in positivity. Overall, I have a positive impression over this paper. I see that it makes a contribution in three ways: First, it focuses on low- and middle-income countries, which may often be disadvantaged in terms of receiving early notification of the virus spread. Second, it provides a practical proof of concept showing evidence of how this approach may be used to track drastic changes in the positivity over a period of time. Third, it provides meaningful discussion on how this approach may can be used in control policy. Reviewer #2: This is an important and relevant paper that looks at the feasibility of wastewater surveillance in a low- and middle-income country. Specifically, in a city with a population of over 10 million where it is estimated that only 2% of households are connected to a reticulated sewerage system, with >95% of wastewater leaking into agricultural fields, rivers, and other groundwater sources. However, there are main concerns that need to be addressed. Main concerns 1- The paper describes how samples were collected and analyzed but there is no data showing RT-qPCR results. The authors should follow: “The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments” (https://academic.oup.com/clinchem/article/55/4/611/5631762) when reporting their results. 2- The results provided by the authors appear correct: - higher positivity rate in wastewater corresponds with clinical data - higher positivity rate for samples from wastewater treatment plans vs rivers and soil However, with out the data described above these results can’t be validated. Minor concerns 1- There are a few typos in the manuscript that suggest that perhaps the authors did not upload the latest version. 2- The resolution of the figures should be improved. 3- A map showing the geographical location of the samples would be helpful to interpret results. ****** 6. 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Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0274793.r001
Revision 1
14 Aug 2022 Author Response Response to Reviewers [PONE-D-22-14874] The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia Editor's comment: As pointed out by one of the reviewers, please describe the data of qPCR. Response to the Editor: We thank you for your interest and positive comments on this paper. In this revised version, we have described the data or RT-qPCR following the MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments, as pointed out by the Reviewer #2. Response to reviewers: Reviewer #1: This paper presents a feasibility study of using wastewater-based epidemiology for early detection of SARS-CoV-2 in low- and middle-income countries. The study is based on 10-week period data collected from key locations. The results show the highest rate of 77% and the lowest rate of 25% in positivity. Overall, I have a positive impression over this paper. I see that it makes a contribution in three ways: First, it focuses on low- and middle-income countries, which may often be disadvantaged in terms of receiving early notification of the virus spread. Second, it provides a practical proof of concept showing evidence of how this approach may be used to track drastic changes in the positivity over a period of time. Third, it provides meaningful discussion on how this approach may can be used in control policy. Response to reviewer #1: We greatly appreciate your positive comments on this paper. Reviewer #2: This is an important and relevant paper that looks at the feasibility of wastewater surveillance in a low- and middle-income country. Specifically, in a city with a population of over 10 million where it is estimated that only 2% of households are connected to a reticulated sewerage system, with >95% of wastewater leaking into agricultural fields, rivers, and other groundwater sources. However, there are main concerns that need to be addressed. Main concerns 1- The paper describes how samples were collected and analyzed but there is no data showing RT-qPCR results. The authors should follow: “The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments” (https://academic.oup.com/clinchem/article/55/4/611/5631762) when reporting their results. Response to reviewer 2: Thank you for pointing out The MIQE Guidelines for reporting RT-qPCR experiments. We provided the information on RT-qPCR experiments such as details of the samples, nucleic acid extraction, reverse transcription, and qPCR target information under the section ‘Laboratory methods for wastewater and environmental samples’ (page 8-10, line 147-186). We also have amended the paper to describe the data and the RT-qPCR as described in the MIQE Guidelines. Furthermore, we have added the median of RT-qPCR cycle threshold data during the 10-week of sample collection for both the N and ORF1ab genes. “The median of cycle threshold (Ct) values for positive N and ORF1ab gene results was 35.1 (IQR: 32.1 – 36.9) and 33.9 (IQR: 30.1 – 35.9), respectively.” (results section, page 11, line 212-214) 2- The results provided by the authors appear correct: - higher positivity rate in wastewater corresponds with clinical data - higher positivity rate for samples from wastewater treatment plans vs rivers and soil However, without the data described above these results can’t be validated. Response to reviewer #2: We found that the changed trends of the positivity rate detected using N and ORF1ab genes were in alignment with confirmed cases in the community. In order to support this result, we attached the distribution maps of SARS-CoV-2 in Yogyakarta, comparing the detection of SARS-CoV-2 targeting N gene to confirmed community cases (Fig 3). The distribution maps illustrate three time points, i.e., week 1-2 (Fig 3A), week 5-6 (Fig 3B) and week 9-10 (Fig 3C). The areas were colored with different shades of blue to depict the number of confirmed COVID-19 cases in community, in which the darker color means the higher confirmed COVID-19 cases. The sampling locations were marked using circles (manholes), pentagons (river) and triangles (NST water) which are colored red if detected as positive or colored green if non-detected. In week 1-2, the COVID-19 cases in the community were high (dark blue), almost all sampling locations were positive for COVID-19 (only two green dots/triangles were shown). As the confirmed cases decreased through time, in week 9-10 the areas were shaded with light blue and the number of sampling locations detected as positive was lower. In addition, we revised the relevant results section to summarize this finding, as below. “The temporal changes in rates of sample positivity correlate with the number of confirmed cases in the community as illustrated in Fig 3. The highest positivity rate of 77%, was obtained for samples collected in July 2021 during week 1 of sample collection and decreased to 25% by the end of September 2021 (corresponding to week 10 of sample collection), reflecting a decreased detection rate correlating with a decrease in the incidence of reported COVID-19 clinical cases in the community.” (results section, page 11, line 216-221) We also added the summary comparing positivity rate between sample types (in results section, page 11, line 214-216) and pie charts of positivity rates of each sample type (Fig 2, see below) to support the finding that river and soil samples showed the lowest positivity rate. “The highest positivity rate was for manhole samples (74%, 191/258 samples, Fig 2) and the lowest was for soil samples (3%, 2/60 samples, Fig 2).” (results section, page 11, line 214-216) Minor concerns 1- There are a few typos in the manuscript that suggest that perhaps the authors did not upload the latest version. Response to reviewer #2: Thank you for pointing out this matter, we have corrected the typos and ensured that the submitted version is the latest version of our work. 2- The resolution of the figures should be improved. Response to reviewer #2: We have re-read the guideline for figures and reviewed our figures following the PLOS ONE requirements using the suggested PACE tool. 3- A map showing the geographical location of the samples would be helpful to interpret results. Response to reviewer#2: The newly attached maps of Fig 3 showing the distribution of SARS-CoV-2 in Yogyakarta have addressed this feedback. This figure is a geographical map of Yogyakarta province. As explained previously, we colored the sub-districts included in this study based on the number of confirmed COVID-19 cases. We also marked the sampling location and gave different symbols to each sample type, i.e., circle (manholes), pentagon (river) and triangle (NST water). https://doi.org/10.1371/journal.pone.0274793.r002
6 Sep 2022 Decision Letter - Etsuro Ito, Editor The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia PONE-D-22-14874R1 Dear Dr. Murni, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Etsuro Ito Academic Editor PLOS ONE 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 #2: All comments have been addressed ******** 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 #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? 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 #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 #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 #2: The authors have addressed all the comments. I believe the figures would benefit from higher resolution. ****** 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 #2: No ******** https://doi.org/10.1371/journal.pone.0274793.r003
Formally Accepted
5 Oct 2022 Acceptance Letter - Etsuro Ito, Editor PONE-D-22-14874R1 The feasibility of SARS-CoV-2 surveillance using wastewater and environmental sampling in Indonesia Dear Dr. Murni: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information please contact onepress@plos.org. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Prof. Etsuro Ito Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0274793.r004

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