Insights into Gastrointestinal Virome: Etiology and Public Exposure

Round 1

Reviewer 1 Report

The review paper focused on enteric virome in infants, etiology of common waterborne enteric viruses (e.g., norovirus, rotavirus, adenovirus…), public exposure to wastewater. However, there was quite limited information and discussion on current knowledge related to enteric viruses in wastewater or environmental waters, their persistence and resistance to water treatment processes, or effective approaches to eliminate the infection risk. Besides, the information about waterborne enteric viruses and their infection risk through wastewater (reuse) are already known and well described in many previous works. So the reviewer concerns about the importance and significance of this current review paper.

 

Other comments

 

Enteric virome in infants (line 25-64)

Regarding the section of enteric virome in infants, the authors provided information and discussed the development and diversity of gastrointestinal virome in infants. But gastrointestinal virome in infants is mainly phages.  Also, the transmission of pathogenic viruses from mothers is not high or significant. So what is the link/relationship between the gastrointestinal virome in infants and waterborne diseases or enteric viruses in wastewater, infection risk through contact with contaminated water (as described in other sections in the manuscript)?

 

Viral etiology (line 65-275)

Five common enteric viruses (AdV, RV, NoV, HAV and AtsV) were selected to describe in the paper. It was likely that the authors more focused on the structure and genotype of these viruses. However, in terms of the waterborne disease or infection risk via contaminated water, it is more interesting to provide information about the presence (frequency and concentration, dominant genotypes) of these viruses in raw and treated wastewater and other water environments.

 

Pubic exposure to municipal wastewater (line 276-292)

people exposed to wastewater by various means (recreational activities, food productions and agriculture), but the infection risk from enteric viruses are dependent on the prevalence of infectious enteric viruses or infectivity of enteric viruses in water environments where people are contacted to. Thus,  It is more interesting to add information or discussion about the infectivity of enteric viruses in water environments.

 

Line 277-278, “The main exposure routes are frequent recreational activities and surface water drinking “.

More information about enteric viruses in recreational activities and surface drinking water should be added.

 

Line 280-281 “Moreover, enteric viruses were detected in 50% to 60 % of the total mussel samples obtained from a bioremediation 281 mussel farm”

Type of enteric viruses, number of the sample tested and detection method (qPCR or cell culture)?, please provide this information

 

Line 294-295, “Wastewater is commonly discharged to surface water resources”

More information about enteric viruses in water sources (surface and groundwater) should be added

Line 300-301 “Wastewater treatment (WWT) performance guidelines have been established for reclamation and reuse “

Please provide the information about the guidelines, particularly its requirement for enteric viruses.

 

Line 308-309, “Additionally, bacteriophage survival in water is more similar to human enteric viruses than the presently used bacterial indicators”

Pepper mild mottle virus and Crassphage have recently been recognized as a good indicator for human enteric viruses in water environments, which are much more suitable than bacteriophage. Please add more information on these viral indicators.

 

Reuse of treated water (line 323-343)

It was likely that the authors focused on wastewater reuse for non-potable purposes such as recreational activities, agriculture and landscape. However, wastewater reuse for potable purposes (especially De facto wastewater reuse) is commonly practiced worldwide. And the risk of viral infection is higher than reuse for non-potable purposes. Thus, it is better to provide information on potable water reuse and the related information on waterborne enteric viruses in this section.

 

Line 318-319, “However, intensive treatment measures are certainly required to meet the suggested wastewater reuse guidelines ”

Please provide more information about the guideline. What is the requirement for wastewater treatment or level of enteric viruses in these guidelines?

 

Line 339-340 “Singapore has approved a potential multi-phase approach to water reuse involving primary sedimentation followed by activated sludge and microfiltration then ultrafiltration, reverse osmosis and eventually disinfection by ultraviolet radiation exposure [190]. This approach can also be highly beneficial to eliminate or even significantly reduce public risks associated with the reuse of various wastewater streams ”

The Water Safety Plan (WSP) is receiving increasing attention as a recommended risk management approach for water reuse. Please also add the concept of WSP.

 

Author Response

Dear respected Reviewer,

I highly appreciate offering time for reviewing our review article and your highly valuable comments. In this regard, kindly find attached the authors' annotated reply for your comments.

Best regards,

Authors 

Author Response File: Author Response.docx

Reviewer 2 Report

General comments: This is a well-written manuscript, short and succinct. Figures are really helpful to the reader. It provides helpful information to a scientific audience. There are minor comments. Nour et al., stated in the abstract that this review manuscript focused primarily in gastrointestinal viral infections in infants, which is not the case as throughout the manuscript the authors described adults, young children, immunocompromised individuals and elderly people. Moreover, survival of these viruses in the environment after wastewater treatment process is conducted is not described. There is also no description of low temperatures. I know the authors made the point of fecal-oral route (aka food ingestion), but the survival of these viruses in wastewater is missing. The paper will make a stronger impact if the survival and potential infection rate is also described for each enteric virus here described.

All the enteric viruses described here are naked viruses. My point is that naked viruses are more resilient to environmental conditions compared to enveloped viruses.

Specific comments are described in the following lines:

Page 1, lines 16-17. Please address my comment above about gastrointestinal infections. You actually described for all patients and not in particular infants.

Page 3, there is no description of Rotavirus survival in the environment as there was for HAdv in Page 2, lines 87-89.

Page 5, lines 173-179. There is description of the temperatures that Norovirus can survive (50-72C and 50-60C), however, these are not temperatures you will find in environmental conditions or during wastewater process.

Page 5, lines 207-218. Same comment as above, the authors aimed to describe about gastrointestinal infections in infants and ended up describing HAV in adults, young children, and elderly. My point, it is not clear if the abstract reflects what is being described in the manuscript body.

Page 6, lines 264-265. The authors keep describing about gastroenteritis in a broad range of ages and not in particular infants. I mean, I do not have problems with that. However, your abstract sounds misleading (as it is mentioned INFANTS).

Page 8, lines 341-343. Please elaborate more about assessment tools. Assessment tools such as? Targeted qPCR, isolation of some of these viruses (I know Noroviruses cannot be cultured so far), sequencing, etc.

Author Response

Dear respected Reviewer,

I highly appreciate offering time for reviewing our review article and your highly valuable comments. In this regard, kindly find attached the authors' annotated reply for your comments.

Best regards,

Authors 

Author Response File: Author Response.docx

Reviewer 3 Report

In this review, authors discussed gastrointestinal virome. Viral etiology and Public exposure were well introduced. However, the text is not well arranged and the logic is not clear. 

1. The title is "Insights into gastrointestinal virome: etiology and public exposure", but in the manuscript only virus infections in infants was discussed.
2. Where are Figure 1 and Figure 2 ?
3. In "Viral etiology" part, authors talked about lots of  knowledge of the basic biology of the virus which has nothing to do with the topic.
4. This manuscript needs careful editing by someone with expertise in technical English editing paying particular attention to English grammar, spelling, and sentence structure so that the goals and results of the study are clear to the reader.
5. "Etiology and public exposure" were not connected in the manuscript.
6. There was no "Conclusion" in the paper.  

 

Author Response

Dear respected Reviewer,

I highly appreciate offering time for reviewing our review article and your highly valuable comments. In this regard, kindly find attached the authors' annotated reply for your comments.

Best regards,

Authors 

Author Response File: Author Response.docx

Reviewer 4 Report

This paper, entitled Insights into gastrointestinal virome: etiology and public exposure, is a scholarly work and can increase knowledge on this domain. The authors provide an interesting manuscript dealing with etiology and public exposure about grastrointestinal virome. The content is relevant to Water and should generate new knowledge, especially with this compilation of information. The manuscript is quite well written and well related to existing literature. Abstract and keywords are meaningful.

I have some general and specific comments:

• Please provide an Introduction section of your work. This section is lacking and shoudl improve greatly the whole quality of your work, allowing to introduce the topic and why this is so important to consider such topic.
• There's no conclusion too, please provide this section.
• Why not considering SARS-Cov2 (Covid19) virus in this review, maybe in discussion? expecially in the current context on pandemic situation, it should be interesting to consider such virus also.
• About reuse of treated water, please provide some details about technical solutions available for this, including a short costs analysis of them and describing efficiency for viral charge removal or bacterial hosts. What are the limitations of reuse (technical, economical, regulation, ...)?

As it, this paper is not fully acceptable for publication in Water and requires minor revision and amendments. I recommend the following decision: ACCETP AFTER MINOR REVISION.

Author Response

Dear respected Reviewer,

I highly appreciate offering time for reviewing our review article and your highly valuable comments. In this regard, kindly find attached the authors' annotated reply for your comments.

Best regards,

Authors 

Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

 

1. Graphical abstract

This graph is a bit complicated and confused. For example:

• Different symbols were used to indicate different enteric viruses à only one symbol to indicate enteric viruses, in general, is enough.
• Bacteria and phage are also present in all types of environmental waters ??
• Symbols of “no virus reduction” and “virus reduction” highly confused readers. Maybe, these symbols can be removed.

 

2. Line 50-51

Please carefully check the information in the reference paper. How the infectivity rate of HAV was higher in treated water than in raw water. Please also indicate the number of samples along with prevalence (%).

 

3. Line 58-59

Potable reuse and De facto reuse are two different definitions of wastewater reuse. Please be careful.

 

4. Please also provide the objectives of this review work in the introduction
5. Line 139-141

The authors provided an additional table “table 1” about adenovirus in various water environments in different countries. So it is better to provide more discussion in the main text about the presence/concentration of adenovirus in environmental waters; how they are similar or different among studies provided in the table.

 

6. Line 160, About Table 1

• Title of table 1: Persistence à occurrence/ presence is more suitable. The table did not provide any information about virus persistence.
• Please check carefully and use a consistent term for “water source” in the table. For example, “Wastewater treatment plant” vs “sewage water” vs “raw water” vs “raw sewage” vs “raw sewage water” vs “WWTP influent”. or “Treated water effluent” vs “WWTP effluent”. Please also check other tables (table 2-6).
• Please check and use a consistent unit of virus concentration. For example, “genome copies/ L” vs “GC/L” vs “genome/L”. Please also check other table (table 2-6).
• It is also more precise to provide the number of sample tested (e.g, positive samples/total samples) along with the frequency (%). Same for other tables.

 

7. Line 181-182,

The authors provided an additional table “table 2” about rotavirus in various water environments in different countries. So it is better to provide more discussion in the main text about the presence/concentration of this virus in environmental waters; how they are similar or different among studies provided in the table.

 

8. Line 252-253

The authors provided an additional table “table 3” about norovirus in various water environments in different countries. So it is better to provide more discussion in the main text about the presence/concentration of this virus in environmental waters; how they are similar or different among studies provided in the table.

 

9. Line 311-313

The authors provided an additional table “table 4” about HAV in various water environments in different countries. So it is better to provide more discussion in the main text about the presence/concentration of this virus in environmental waters; how they are similar or different among studies provided in the table.

 

10. Line 360-361

The authors provided an additional table “table 5” about Astrovirus in various water environments in different countries. So it is better to provide more discussion in the main text about the presence/concentration of this virus in environmental waters; how they are similar or different among studies provided in the table.

 

11. Line 360-361

The authors provided an additional table “table 6” about the infectivity of viruses in water sources. So it is better to provide more discussion in the main text about the infectivity of viruses in environmental waters.

 

12. Line 414 about the table 6.

• Please also provide the virus detection method. All mentioned studies applied cell culture method ??.
• What do authors mean “infectivity rate” column? Detection frequency??. Please also provide the number of samples tested.
• The reviewer could not understand the information of “infection risk (IR)” column. What is the meaning of infection risk reduction (including period and reduction amount) here?. The information in this column confused readers.

 

13. Line 398-411

Authors did not focus on SARS-CoV-2 as common viruses (e.g., AdV, NoV, AstV, RV, HAV) in the earlier section, therefore, it is better to shorten the information of SARS-CoV-2 in this section. Or authors want to focus on SARS-CoV-2, please consider making a separate section to discuss about SARS-CoV-2 in waters.

 

 

14. Line 398-399,

“(Figure 4) prevalence and infectivity using different genes”. Infectivity??. Figure 4 did not show the virus infectivity. Some studies tried to investigate the infectivity of SARS-CoV-2 by using capsid integrity RT-qPCR. Authors can consider using this information.

https://doi.org/10.1016/j.scitotenv.2021.148342

https://doi.org/10.1038/s41598-021-97700-x

 

15. Line 400-401

“highest SARS-CoV-2 detection specificity was obtained when RdRP was applied”. Please provide the reference for this. Normally, to detect SARS-CoV-2 in water, CDC N1 primer is more commonly used.

 

16. Line 403-404

“Higher SARS-CoV-2 concentration was found in treated wastewater (19.85 GE/ml) rather than 11.5 GE/ml in raw sewage”.  The concentration in treated wastewater should not be higher than the concentration in raw wastewater. Besides, 19.85 GE/mL and 11.5 GE/mL just mean no difference in the concentration. Please check the information and revise the sentence.

 

17. Line 542-567

About the conclusion section. Detailed discussion (e.g., prevalence or concentration of viruses) or new (undiscussed) information (e.g., ICC-qPCR method) should not be mentioned in the conclusion part. Please consider rearranging the information or move some information to the above sections.

Author Response

Dear Respected Reviewer,

Thanks a lot for offering time for reviewing our paper for the second time. Your valuable were highly appreciated. Kindly, find attached "Reviewer comments and author replies" file attached for your consideration.

Best regards,

Authors

Author Response File: Author Response.docx

Reviewer 3 Report

There was no author`s reply to my last review comments.

Author Response

Dear Respected Reviewer,

Thanks a lot for offering time for reviewing our article and for your highly worthy comments.

Best regards,

Authors

Author Response File: Author Response.docx

Round 3

Reviewer 3 Report

I suggest authors reduce some content of basic biochemical  knowledge of viruses. Then the manuscript can be accepted.

Author Response

Dear Respected Reviewer,

Thanks a lot for offering time for reviewing our paper for the second time. Your valuable were highly appreciated. Kindly, find attached "Reviewer comment and author reply" file attached for your consideration.

Best regards,

Authors

Author Response File: Author Response.docx