Cycle Threshold Values of SARS-CoV-2 RT-PCR during Outbreaks in Nursing Homes: A Retrospective Cohort Study

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

I appreciate the opportunity to review this interesting article. This is a retrospective cohort study evaluating the usefulness of Ct values from RT-PCR testing for SARS-CoV-2 in nursing homes. The introduction provides an appropriate theoretical framework, highlighting the potential usefulness of Ct values and justifying them in the context of nursing homes and the limited information available on the subject. The methodology is described in detail, as is the presentation of the results. The discussion compares the results with what has been reported in the international literature to date. The limitations and strengths of the study are described in detail. There are only a few observations:

-In the Materials and Methods section, it would be worthwhile to describe clearly and in detail the inclusion and exclusion criteria used for patient selection.

-Regarding the lack of ethics committee approval, I think it would be appropriate for the authors to elaborate on this justification. Although the data belong to the Ministry of Health (or similar agency) of the country, they were collected for epidemiologic use, not for research use, and therefore there must be at least an approval from the ethics committee to use them for this purpose, in accordance with good clinical practice.

-I believe that the conclusions section should be expanded to include the authors' opinions on the subject studied and future directions.

Author Response

Review 1.

I appreciate the opportunity to review this interesting article. This is a retrospective cohort study evaluating the usefulness of Ct values from RT-PCR testing for SARS-CoV-2 in nursing homes. The introduction provides an appropriate theoretical framework, highlighting the potential usefulness of Ct values and justifying them in the context of nursing homes and the limited information available on the subject. The methodology is described in detail, as is the presentation of the results. The discussion compares the results with what has been reported in the international literature to date. The limitations and strengths of the study are described in detail. There are only a few observations:

Thank you very much for your comments about our study. We have followed your observations and made all the suggested changes.

-In the Materials and Methods section, it would be worthwhile to describe clearly and in detail the inclusion and exclusion criteria used for patient selection.

We add the inclusion and exclusion criteria following your indication.

-Regarding the lack of ethics committee approval, I think it would be appropriate for the authors to elaborate on this justification. Although the data belong to the Ministry of Health (or similar agency) of the country, they were collected for epidemiologic use, not for research use, and therefore there must be at least an approval from the ethics committee to use them for this purpose, in accordance with good clinical practice.

We add the references of the Spain legislation and regulations about this issue, that include the General Law of Health, the Law of Cohesion and Quality of the National System of Health,  the Law General of Public Health], and the Early Response Plan in a COVID-19 Pandemic Control Scenario.

I believe that the conclusions section should be expanded to include the authors' opinions on the subject studied and future directions.

We appreciate your suggestion, and we have added commentary of this subject on the final of the discussion.

Reviewer 2 Report

Comments and Suggestions for Authors

A report of a retrospective study of four nursing homes in the Health Department of Castellon, Spain, during 2020-2022 to know the Ct values regarding the incidence and reinfection of the SARS-CoV-2 virus in successive outbreaks. The purpose is to test its usefulness for epidemic surveillance in nursing homes. In finding that hybrid immunity suggests a decrease in the transmission and severity, this tool is relevant for epidemiological surveillance of the virus in nursing homes.

 

The work is well-conceptualized, well-researched, well-referenced, well-analyzed, and well-written. The weaknesses are insufficient information regarding the selection of methods, and the tables need layout improvement. The suggestion is to include a hypothesis. 

 

Line by line suggested edits.

40-41 As the authors cite only four studies, add more studies to demonstrate that there are “many” or another option is to change “have been considered in the diagnosis, follow-up, and infectivity of SARS-CoV-2 in many studies” to “have been well-considered in the diagnosis, follow-up, and infectivity of SARS-CoV-2 studies”.  

67 The authors have listed no hypothesis.  Although this is not imperative, there would be improvement to the manuscript with a tested hypothesis.

75 Please state here that informed consent was not required because this was a retrospective study.

91-92 Please explain the selection of these variable comparisons with these tests and cite similar studies using the same tests.

103 As citation 27 is outdated, please include a COVID-19 publication using the DAGs method. Please also explain the selection of the Stata® program 14 version 2 used for the statistical analysis and cite COVID-19-related research using the same program.

126-127 Table 1—Please eliminate the first row, “Nursing homes”, and underline what is currently the second row to become the first row. Given that all the percentages are on the same line as the data for each entry, please put “N (%)” on the same line as “Centre [n]”  and “Total” for the heading. Additional space to do this is by making those entries under “Variables” that stretch to two lines be of equal length, rather than the first line expanding the width of the column, as it does now. For the entries under “Variables” that cover more than two lines, “days” is in round brackets. Since the authors have used round brackets in the entries for percentages, and the days in the entries are not in round brackets, change “(days)” to “in days”. This point is also relevant to the lines with “(%)”. Change to “%”. Another point is to change “SARS-COV-2” to “SARS-CoV-2”, as it appears in the majority of the entries under “Variables”. The final point is to change “7   (5.6)” to “7 (5.6)”.

145-146 Table 2—Please eliminate the first row, “Nursing homes”, and underline what is currently the second row to become the first row. Given that all the percentages are on the same line as the data for each entry, please put “N (%)” on the same line as “Centre [n]”  and “Total” for the heading. Given the space between the Variables column and the others, there is sufficient space to do this. Change “Residents     with PCR-Ct” to “Residents with PCR-Ct”.

156-157 Table 3—Please eliminate the first row of “Cycle thresholds” and underline what is currently the second row to become the first row. Although the first two columns of entries on the left will have two-line titles, in this instance, it is acceptable. Please head the left-most column as “Variables”.

165-166 Table 4— Please eliminate the first row, “Reinfections”, and underline what is currently the second row to become the first row. Although the first two columns of entries on the left will have two-line titles, in this instance, it is acceptable. Change the title “Cycle threshold” to “Cycle threshold—reinfections”.

168 If the authors decide to include a hypothesis in the Introduction, please begin the Discussion section by considering the hypothesis.

232 Please include suggested future research directions.

326 Please make “2022” bold.

349 Please make “2016” bold.

Author Response

Review 2

A report of a retrospective study of four nursing homes in the Health Department of Castellon, Spain, during 2020-2022 to know the Ct values regarding the incidence and reinfection of the SARS-CoV-2 virus in successive outbreaks. The purpose is to test its usefulness for epidemic surveillance in nursing homes. In finding that hybrid immunity suggests a decrease in the transmission and severity, this tool is relevant for epidemiological surveillance of the virus in nursing homes.

 

The work is well-conceptualized, well-researched, well-referenced, well-analyzed, and well-written. The weaknesses are insufficient information regarding the selection of methods, and the tables need layout improvement. The suggestion is to include a hypothesis. 

 

We are grateful for your comments and suggestions about our manuscript.

 

Line by line suggested edits.

40-41 As the authors cite only four studies, add more studies to demonstrate that there are “many” or another option is to change “have been considered in the diagnosis, follow-up, and infectivity of SARS-CoV-2 in many studies” to “have been well-considered in the diagnosis, follow-up, and infectivity of SARS-CoV-2 studies”.

 

Thank you very much for your suggestions and proposed alternatives. We opt to add five more studies considering the importance of this issue.

 

  

67 The authors have listed no hypothesis.  Although this is not imperative, there would be improvement to the manuscript with a tested hypothesis.

 

We appreciate your suggestion, and we add the hypothesis of the research.

Our hypothesis was that SARS-CoV-2 reinfection plus SARS-CoV-2 (hybrid immunity) could offer better protection against severe disease and viral transmission, and this could be measured by Ct values.  

 

75 Please state here that informed consent was not required because this was a retrospective study.

We include your comment in the manuscript.

 

91-92 Please explain the selection of these variable comparisons with these tests and cite similar studies using the same tests.

 

Thank you very much for your indications. We explain the selection of variables following the Directed Acyclic Graphs, and we have changed some phrases. In addition, we have added some studies using multivariable linear regression and COVID-19.

 

 

103 As citation 27 is outdated, please include a COVID-19 publication using the DAGs method. Please also explain the selection of the Stata® program 14 version 2 used for the statistical analysis and cite COVID-19-related research using the same program.

 

Thank you very much for your indication

We have included two studies of COVID-19 and DAGs, also COVID-19 and STATA®

 

126-127 Table 1—Please eliminate the first row, “Nursing homes”, and underline what is currently the second row to become the first row. Given that all the percentages are on the same line as the data for each entry, please put “N (%)” on the same line as “Centre [n]”  and “Total” for the heading. Additional space to do this is by making those entries under “Variables” that stretch to two lines be of equal length, rather than the first line expanding the width of the column, as it does now. For the entries under “Variables” that cover more than two lines, “days” is in round brackets. Since the authors have used round brackets in the entries for percentages, and the days in the entries are not in round brackets, change “(days)” to “in days”. This point is also relevant to the lines with “(%)”. Change to “%”. Another point is to change “SARS-COV-2” to “SARS-CoV-2”, as it appears in the majority of the entries under “Variables”. The final point is to change “7   (5.6)” to “7 (5.6)”.

 

Thank you very much. We have made the suggested changes.

 

145-146 Table 2—Please eliminate the first row, “Nursing homes”, and underline what is currently the second row to become the first row. Given that all the percentages are on the same line as the data for each entry, please put “N (%)” on the same line as “Centre [n]”  and “Total” for the heading. Given the space between the Variables column and the others, there is sufficient space to do this. Change “Residents     with PCR-Ct” to “Residents with PCR-Ct”.

 

Thank you very much. We have followed your indications.

 

156-157 Table 3—Please eliminate the first row of “Cycle thresholds” and underline what is currently the second row to become the first row. Although the first two columns of entries on the left will have two-line titles, in this instance, it is acceptable. Please head the left-most column as “Variables”.

 

Thank you very much. We have followed your indications.

 

 

165-166 Table 4— Please eliminate the first row, “Reinfections”, and underline what is currently the second row to become the first row. Although the first two columns of entries on the left will have two-line titles, in this instance, it is acceptable. Change the title “Cycle threshold” to “Cycle threshold—reinfections”.

 

Thank you very much. We have followed your indications.

 

168 If the authors decide to include a hypothesis in the Introduction, please begin the Discussion section by considering the hypothesis.

 

We have added a new phrase with our hypothesis.

 

232 Please include suggested future research directions.

 

We appreciated for your suggestion. We have indicated future research lines.  

 

326 Please make “2022” bold. We correct the mistake..

 

349 Please make “2016” bold. We correct the mistake.

 

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

I thank the authors for taking my observations and comments into account. With the added information and the clarification of ethical issues, I believe that my observations have been resolved and that the article meets the criteria for consideration for publication.