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Research Article
Revised

Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020

[version 4; peer review: 2 approved]
PUBLISHED 24 Nov 2021
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This article is included in the Cell & Molecular Biology gateway.

Abstract

Background: Sapovirus has emerged as a viral cause of acute gastroenteritis. However, there is limited data on sapovirus in Egypt. . The present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis <5 years in Mansoura, Egypt from January 2019 to February 2020 by reverse transcriptase-polymerase chain reaction (RT-PCR).
Methods: The cross-sectional study enrolled a 100 children <5 years who presented with acute gastroenteritis at an outpatient clinic in Mansoura, Egypt between January 2019 and February 2020. Clinical data, demographic data and a stool sample was collected from each child. Stools were screened by microscopy for parasites and culture methods for bacteria and excluded from the study if positive for either. Specimens were also screened for rotavirus by enzyme immune assays (EIA) and sapovirus by reverse transcription PCR.
Results: The most frequently detected virus was rotavirus by ELISA 25% (25/100). RT-PCR detected sapovirus in 7% (7/100) of the stool samples. The children with sapovirus were all from rural regions and presented mainly during the winter season in Egypt 42.9% (3/7). The main presenting symptoms were fever 71.4% (5/7) and vomiting 57.1% (4/7). None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in  five samples (5/7) , 71.4%, P=0.01.
Conclusion: The present study highlights the emergence of sapovirus as a frequent pathogen associated with acute gastroenteritis in children. There is a need for a national survey program for the study of sapovirus among other pathogens associated with acute gastroenteritis for better management of such infection.

Keywords

sapovirus

Revised Amendments from Version 3

Author Response to the reviewer
Thanks Sir for your effort for the revision.
Discussion, paragraph 1: Please rather use low-income, middle-income or high-income as these have been defined by the World Bank rather than underdeveloped which is not specific or well defined. This correction was noted in the previous review and has not been full corrected.
Corrected
 Discussion, paragraph 2: Please delete the word hospital. The previous review indicated that either outpatient or hospital should be retained and the other word deleted as it was unclear where the study was conducted.
Deleted
Discussion, paragraph 3, line 3 states "A previous systematic review of sapovirus in African countries revealed that rotavirus..." Not sure why the authors are referring to a sapovirus paper for rotavirus prevalence and the reference used for the study is incorrect - should more likely be 4 or 24 and not 14. Please correct the sentence and the reference.
A reference was corrected

See the authors' detailed response to the review by Marta Diez Valcarce
See the authors' detailed response to the review by Nicola A. Page

Introduction

Sapovirus is a single strand non enveloped RNA virus that belongs to the Caliciviridae family14. The length of its genome is 7.1 to 7.7 kb, and its polyadenylated 3’ terminal is responsible for viral replication, while its 5’ terminal is associated with viral translation through production of VPg5,6. The viral genome consists of two to three open reading frames5. There are 15 genogroups of the virus with only four of them can infect humans, namely GI, GII, GIV and GV)2,5,7,8.

The laboratory methods for detection of sapovirus include enzyme-linked immunosorbent assay, electron microscopy, reverse transcription-polymerase chain reaction (RT-PCR) and next-generation sequencing3. The sensitivity and specificity of RT-PCR are good and can be used for routine identification of the virus3. The sensitivity and specificity of most RT-PCR detection assays for sapovirus are above 90%9,10. The primers used for the amplification of the virus depend upon the use of a segment from capsid region3,11. The classification of sapovirus depends upon complete sequence analysis of VP16,12,13.

Diarrhea represents the second common cause of death in children and is associated with about 525 000 deaths around the world14. Sapovirus gastroenteritis occurs via ingestion of contaminated food and water and also by direct contact with affected individuals1316. The infection occurs both sporadically and as an outbreak2,11. Treatment is symptomatic to prevent the aggravation of the disease3,11, and prevention of the infection depends mainly upon access to clean drinking water and food and on good hygiene habits (WHO’s five keys to food safety) and hand washing17.

There are data available about sapovirus infection in different countries such as Peru18 Iran19 and Ethiopia20. There is limited data on sapovirus in Egypt. Therefore, the present study aimed to evaluate the presence of sapovirus in children with acute gastroenteritis by RT-PCR.

Methods

Study design and participants

The cross-sectional study enrolled 100 children <5 years who presented with acute gastroenteritis at an outpatient clinic in Mansoura, Egypt between January 2019 and February 2020. Clinical data, demographic data and a stool sample was collected from each child. Stools were screened by microscopy for parasites and culture methods for bacteria and excluded from the study if positive for either. Specimens were also screened for rotavirus by enzyme immune assays (EIA) and sapovirus by reverse transcription PCR.

The procedures followed were approved by the Mansoura Faculty of Medicine, Egypt ethical committee on human experimentation (R.20.11.1053) and were carried out in accordance with the Helsinki Declaration of 1975, as revised in 1983. Written informed consent was obtained from the parents of the included children.

Each child was subjected to full medical history by asking the parents about the residence area and age of the child, which was then followed by clinical examination. A stool sample was collected from each child for laboratory examination.

Stool samples

Each stool sample was subjected to study by direct microscopic examination, study for rotavirus by ELISA Ridascreen® (R-Biopharm AG- An der Neuen Bergstraße 1764297 Darmstadt, Germany), and the remaining samples was subjected to RNA extraction and RT-PCR for sapovirus.

ELISA for rotavirus. The ELIA was completed according to the manufacturer’s instructions with EIA plates read at 450nm on a Statfax Chromate 4300 (Unit No. 518, 5th Floor, MGF Metropolis Mall, MG Road, Gurgaon, Haryana-122002).

Sapovirus PCR

Extraction of RNA and complementary DNA preparation. The stool samples were subjected to the extraction of RNA of sapovirus using QIAamp Viral RNA kit (Qiagen). The extraction was performed according to the instructions supplied by the manufacturer.

Reverse transcriptase

A total volume of reaction mixture were prepared by adding 7.5 µl of extracted RNA to 2.05 µl 5× First-Strand Buffer (Invitrogen-USA), 0.75 µl of 10 mM dNTPs (Qiagen-USA), 0.375 µl (1 µg/ µl) of random primer (Qiagen-USA), 0.75 µl of 10 mM DTT (Invitrogen), 0.5 µl of RNase Inhibitor (Qiagen-USA), and 0.75 µl (200 U/ µl) of SuperScript Reverse Transcrip tase II (Thermofisher-USA). MilliQ water was added to give a total volume of 15.0 µl.

PCR for sapovirus. The amplification process was carried out using previously reported primers with nucleotide sequences of primers as follows: SLV5749 forward 5’-CGGRCYTCAAAVSTACCBCCCCA-3’; SLV5317 reverse 5’- CTCGCCACCTACRAWGCBTGGTT-3’9.

The cDNA generated from the previous step was used as 2.5 µl and added to ready to use amplification mixture supplied from Qiagen with 0.4 µl of the used primers in total volume 25 µl. The amplification procedures were performed using the following conditions: denaturation at 94°C for 5 minutes, then 35 cycles composed of 94°C for 45 seconds- 55°C for 45 seconds and 72°C for 1 minute, then final extension of 7 minutes at 72°C (MiniAmp Thermal Cycler, Applied Biosystem).

PCR products were visualized under UV illumination after electrophoresis on a 1% agarose gel stained with ethidium bromide. The estimated amplified fragment size for sapovirus was 434 bp9.

Statistical analysis

Data were analysed with SPSS 22 (SPSS Inc, Chicago, Illinois, USA). Quantitative values were calculated as numbers and percentages. The use of the chi-square test performed comparisons, and the P-value was considered significant if it was <0.05.

Results

The study included 100 children with AGE manifested by diarrhoea associated predominately with fever (56%) 56/100, vomiting (47%) 47/100, abdominal pain (42%) 42/100. A minority had dehydration (11%) 11/100. Their mean age± SD was 53.33± 11.71 months. Most cases presented in the spring season (34%) 34/100 followed by winter (24%) 24/100. Demographics of the children are shown in Table 1.

Table 1. Demographic and clinical data of the studied children (n=100).

Parameter
Age, months (mean± SD)53.33± 11.71
Gender, n (%)
Male
Female

66 (66)
34 (34)
Season, n (%)
Summer (21 Ęune-22 September)
Autumn (23 September-21 December)
Winter (22 December-19 March)
Spring (20 March-20 Ęune)

20 (20)
22 (22)
24 (24)
34 (34)
Residence, n (%)
Rural
Urban

68 (68)
32 (32)
Abdominal pain, n (%)42 (42)
Fever, n (%)56 (56)
Vomiting, n (%)47 (47)
Dehydration, n (%)11 (11)

The most frequently detected virus was rotavirus by ELISA (25%) 25/100. RT-PCR detected sapovirus in seven samples 7% 7/100 of the stool samples.

The children with sapovirus were all from rural regions (Belkas, Dekrnes, Aga) and presented mainly during the winter season (22 December–19 March) in Egypt in three children (42.9%) 3/7. The main presenting symptoms were fever in five children (71.4%) 5/7 and vomiting in four children (57.1%) 4/7. None of the children with sapovirus had dehydration. Rotavirus was significantly associated with sapovirus infections in five children (71.4%, P=0.01) 5/7 (Table 2).

Table 2. Comparison between sapovirus positive children and sapovirus negative children.

Sapovirus
positive
(n=7)
Sapovirus
negative
(n=93)
Odds
ratio
95%CIP-value
n (%)
Gender
Male
Female

4 (57.1)
3 (42.9)

62 (66.7)
31 (33.3)

0.667

0.14-3.155

0.61
Age, months (mean± SD)48.86± 9.4051.52± 11.880.6
F=0.33
Rural residence7 (100)61 (65.6)0.8970.828-0.9720.09
Season
Summer (21 Ęune-22 September)
Autumn (23 September-21 December)
Winter (22 December-19 March)
Spring (20 March-20 Ęune)

0 (0)
2 (28.6)
3 (42.9)
2 (28.6)

20 (21.5)
20 (21.5)
21 (22.6)
32 (34.4)

1.55

0.32-7.315

0.41
Vomiting4 (57.1)43 (46.2)1.60.32-7.310.7
Abdominal pain2 (28.6)40 (43.01)0.530.1-2.870.69
Fever5 (71.4)51 (54.8)2.0590.38-11.1570.46
Dehydration0 (0)11 (11.8)1.0851.02-1.150.43
Rotavirus5 (71.4)20 (21.5)9.121.646-50.5940.01

Discussion

Viral pathogens represent a significant aetiology for acute gastroenteritis. These infections are usually self-limited in high income countries while it may lead to mortality in low income countries, especially in children15,21.

The present study including children <5 with diarrhea in an outpatient setting showed that the majority of cases experienced fever, vomiting and abdominal pain; common symptoms of viral gastroenteritis. These patients usually present to outpatient clinics and do not require hospital admission except in rare instance of dehydration. The findings support the results noted in previous study22.

The proper management of children with AGE relies upon appropriate and robust diagnosis of the aetiology. In the present study, the most frequently detected virus was rotavirus by ELISA (25%). A previous systematic review in African countries revealed that rotavirus is associated with AGE in 31.5% of children and 25.7% in the general population16. Previous studies in Africa reported that the prevalence of rotavirus infections ranged from 22.73% up to 30% in children below 5 years23,24. The study of rotavirus in Africa was carried out from 2006 to 2008 in 11 African countries and 2200 samples out of 5461 stool was positive for rotavirus24. A previous study pubkished 2018 from Abu El-reesh hospital in Cairo, Egypt reported that the prevalence of rotavirus was 31% among 119 hospitalized children below 5 years with AGE25.

The study of sapovirus as an emerging pathogen associated with AGE has gained importance in recent years. Research has been facilitated by the emergence of the molecular techniques in laboratory diagnosis18,26,27. In the present study, sapovirus was detected among 7% of children with AGE by RT-PCR. A previous meta-analysis study reported that the prevalence of sapovirus was 6.5% with a remarkable difference in the presence of sapovirus between low income and high-income countries28. Another study reported a lower prevalence of sapovirus 4.6% (10/219)28. The incidence of sapovirus infection in a study from Puru published in 2018 in the first and second years of life was 4.3 and 11.1 per 100 child-months, respectively18. In a case-control study from United states of America published 2019 in 300 children below 2 years with AGE versus 272 matched healthy control the prevalence of sapovirus was 7.0% versus 3.0% (P = .07)29. The variation of the prevalence rates reported may be due to the variation of the climate, environment, socio-economic factors, and cultural practices beside the difference of the used method of diagnoses.

The treatment of sapovirus depends mainly upon oral rehydration solution and zinc supplementation30. The risk factors for sapovirus infection are not fully understood. The prevention of sapovirus infection depends mainly upon efficient hand hygiene practice, environmental disinfection, proper sewage disposal, and limited contact with ill individuals. There are conflicting data about the role of improvement of water sanitation in the prevention of sapovirus as it is a common pathogen in both high and low-income countries. However, as it is transmitted by contaminated water and food31, improving food safety and access to clean water and improved sanitation services will reduce the burden of the infection.

The use of new molecular technologies for sapovirus detection in different samples from patients, food and environment, is important to recognize the mode of sapovirus transmission. Infection at a young age may predispose to durable immunity. Therefore, the development of a vaccine toward this virus may reduce the burden of this infection32.

In the present study, there was no significant difference between the clinical presentation of sapovirus positive and sapovirus negative children. The clinical symptoms associated with AGE usually include diarrhoea, vomiting, and fever, making laboratory diagnosis essential for appropriate management. Therefore, there is a need for a national survey program to improve the monitoring of the circulation of enteric viruses including sapovirus alongside other pathogens associated with gastroenteritis to improve the control measures32.

Conclusions

The present study highlights the presence of sapovirus as a pathogen associated with AGE in children from Mansoura, Egypt during 2019 and 2020. There is a need for a national survey program for the study of sapovirus among other pathogens association with AGE for better management of such infection.

Data availability

Underlying data

Figshare: Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study, https://doi.org/10.6084/m9.figshare.13574933.v133

Data are available under the terms of the Creative Commons Attribution 4.0 International license (CC-BY 4.0).

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Zaki MES, Shrief R and Hassan RH. Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.12688/f1000research.29991.4)
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Version 4
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PUBLISHED 24 Nov 2021
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Reviewer Report 29 Nov 2021
Nicola A. Page, Center for Enteric Diseases, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa 
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All corrections ... Continue reading
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Page NA. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.79575.r101105)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Reviewer Report 25 Nov 2021
Marta Diez Valcarce, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA 
Approved
VIEWS 4
After the revisions I ... Continue reading
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HOW TO CITE THIS REPORT
Diez Valcarce M. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.79575.r101104)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Reviewer Report 16 Nov 2021
Nicola A. Page, Center for Enteric Diseases, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa 
Approved with Reservations
VIEWS 5
The revised paper has been improved in the current version and describes the detection of sapovirus in children under five presenting to an outpatient clinic for the treatment of diarrhoea between January 2019 and February 2020 in Mansoura, Egypt. 
... Continue reading
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Page NA. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.77735.r99618)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 19 Nov 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    19 Nov 2021
    Author Response
    Author Response to the reviewer
    Thanks Sir for your effort for the revision.
    • Discussion, paragraph 1: Please rather use low-income, middle-income or high-income as these have been defined
    ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 19 Nov 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    19 Nov 2021
    Author Response
    Author Response to the reviewer
    Thanks Sir for your effort for the revision.
    • Discussion, paragraph 1: Please rather use low-income, middle-income or high-income as these have been defined
    ... Continue reading
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Reviewer Report 02 Nov 2021
Marta Diez Valcarce, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA 
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I accept the manuscript ... Continue reading
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Diez Valcarce M. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.56913.r85957)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
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Reviewer Report 14 Sep 2021
Nicola A. Page, Center for Enteric Diseases, National Institute for Communicable Diseases (NICD), Johannesburg, South Africa 
Approved with Reservations
VIEWS 12
The paper describes the EIA screening of rotavirus and RT-PCR detection of sapovirus in 100 children with acute diarrhoea enrolled from outpatient clinics in Mansoura, Egypt between January 2019 and February 2020. Children with bacterial or parasite infections were excluded ... Continue reading
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Page NA. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.56913.r93206)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 09 Nov 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    09 Nov 2021
    Author Response
    Thanks for the reviewer comments and for the time to review the article. I have made the required changes
     
    • When reporting viral epidemiology, authors should include person,
    ... Continue reading
COMMENTS ON THIS REPORT
  • Author Response 09 Nov 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    09 Nov 2021
    Author Response
    Thanks for the reviewer comments and for the time to review the article. I have made the required changes
     
    • When reporting viral epidemiology, authors should include person,
    ... Continue reading
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Reviewer Report 12 May 2021
Marta Diez Valcarce, Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA 
Approved with Reservations
VIEWS 27
The article titled 'Molecular study of sapovirus in acute gastroenteritis in children: a cross-sectional study' by El Sayed Zaki et al. includes some very interesting data on the prevalence of sapovirus in Egypt.

Overall, the article is ... Continue reading
CITE
CITE
HOW TO CITE THIS REPORT
Diez Valcarce M. Reviewer Report For: Molecular Detection of Sapovirus in Children Under Five Years with Acute Gastroenteritis in Mansoura, Egypt between January 2019 and February 2020 [version 4; peer review: 2 approved]. F1000Research 2021, 10:123 (https://doi.org/10.5256/f1000research.33041.r83889)
NOTE: it is important to ensure the information in square brackets after the title is included in all citations of this article.
  • Author Response 24 May 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    24 May 2021
    Author Response
    Dear Dr. Diez Valcarce, 

    Thanks for your valuable comments. I have made all the required corrections.

    Best Regards.
    Competing Interests: No competing interests were disclosed.
COMMENTS ON THIS REPORT
  • Author Response 24 May 2021
    Maysaa El Zaki, Clinical Pathology Department, Faculty of Medicine, Mansoura Faclty of Medicine, Mansoura, 35516, Egypt
    24 May 2021
    Author Response
    Dear Dr. Diez Valcarce, 

    Thanks for your valuable comments. I have made all the required corrections.

    Best Regards.
    Competing Interests: No competing interests were disclosed.

Comments on this article Comments (0)

Version 4
VERSION 4 PUBLISHED 17 Feb 2021
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Approved - the paper is scientifically sound in its current form and only minor, if any, improvements are suggested
Approved with reservations - A number of small changes, sometimes more significant revisions are required to address specific details and improve the papers academic merit.
Not approved - fundamental flaws in the paper seriously undermine the findings and conclusions
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