Genotyping of Rotaviruses in River Nile in Giza, Egypt

Overview

Journal Iran J Public Health

Date 2020 Apr 21

PMID 32309236

Citations 1

Authors

Neveen Magdy Rizk

Abdou Kamal Allayeh

Affiliations

Soon will be listed here.

Abstract

Background: In 2013, WHO estimated the annual diarrheal mortality rate among children less than five years in Egypt was 24 deaths per 100.000, 2% was due to rotavirus infection.

Methods: Eight water samples were collected monthly from the Nile water stream passing through Giza over 12 months during June 2016 to May 2017. Totally, ninety-six water samples were collected and concentrated for the detection of rotavirus group A (RV-A) using RT-PCR. Multiplex semi-nested RT-PCR was performed to identify the genotypes P and G of RV-A.

Results: The detection rate of RV-A was 18.75% (18/96), whereas the rate of rotavirus genotypes G and P were 61% (11/18) and 50% (9/18), respectively. Rotaviruses G1P[8] and G1P[4] were the most common genotypes identified in our survey. In addition, the seasonal distribution findings demonstrated that the highest detection rate was 37.5% in the winter season, followed by 20.8%, 12.5% and 4% in spring, autumn and summer, respectively.

Conclusion: Multiplex semi-nested RT-PCR is a useful method for rapid detection and genotyping of RV-A in surface water samples.

Citing Articles

Occurrence of Human Enteric Viruses in Water Sources and Shellfish: A Focus on Africa.

Upfold N, Luke G, Knox C Food Environ Virol. 2021; 13(1):1-31.

PMID: 33501612 PMC: 7837882. DOI: 10.1007/s12560-020-09456-8.

References

Matson D, Abdel-Messih I, Schlett C, Bok K, Wienkopff T, Wierzba T . Rotavirus genotypes among hospitalized children in Egypt, 2000-2002. J Infect Dis. 2010; 202 Suppl:S263-5. DOI: 10.1086/653581. View

Katukiza A, Temanu H, Chung J, Foppen J, Lens P . Genomic copy concentrations of selected waterborne viruses in a slum environment in Kampala, Uganda. J Water Health. 2013; 11(2):358-70. DOI: 10.2166/wh.2013.184. View

Koroglu M, Yakupogullari Y, Otlu B, Ozturk S, Ozden M, Ozer A . A waterborne outbreak of epidemic diarrhea due to group A rotavirus in Malatya, Turkey. New Microbiol. 2011; 34(1):17-24. View

Shoeib A, Hull J, Jiang B . Rotavirus G and P types in children with acute diarrhea in Cairo, Egypt, 2011-2012. J Egypt Public Health Assoc. 2015; 90(3):121-4. DOI: 10.1097/01.EPX.0000470849.84604.13. View

Petrinca A, Donia D, Pierangeli A, Gabrieli R, Degener A, Bonanni E . Presence and environmental circulation of enteric viruses in three different wastewater treatment plants. J Appl Microbiol. 2009; 106(5):1608-17. DOI: 10.1111/j.1365-2672.2008.04128.x. View

Onda K, Lobuglio J, Bartram J . Global access to safe water: accounting for water quality and the resulting impact on MDG progress. Int J Environ Res Public Health. 2012; 9(3):880-94. PMC: 3367284. DOI: 10.3390/ijerph9030880. View

El-Senousy W, Ragab A, Handak E . Prevalence of Rotaviruses Groups A and C in Egyptian Children and Aquatic Environment. Food Environ Virol. 2015; . DOI: 10.1007/s12560-015-9184-6. View

Afrad M, Hassan Z, Farjana S, Moni S, Barua S, Das S . Changing profile of rotavirus genotypes in Bangladesh, 2006-2012. BMC Infect Dis. 2013; 13:320. PMC: 3723515. DOI: 10.1186/1471-2334-13-320. View

Kittigul L, Panjangampatthana A, Rupprom K, Pombubpa K . Genetic diversity of rotavirus strains circulating in environmental water and bivalve shellfish in Thailand. Int J Environ Res Public Health. 2014; 11(2):1299-311. PMC: 3945539. DOI: 10.3390/ijerph110201299. View

10.

Chaimongkol N, Khamrin P, Malasao R, Thongprachum A, Ushijima H, Maneekarn N . Genotypic linkages of gene segments of rotaviruses circulating in pediatric patients with acute gastroenteritis in Thailand. Infect Genet Evol. 2012; 12(7):1381-91. DOI: 10.1016/j.meegid.2012.04.015. View

11.

Saudy N, Elshabrawy W, Megahed A, Foad M, Mohamed A . Genotyping and Clinicoepidemiological Characterization of Rotavirus Acute Gastroenteritis in Egyptian Children. Pol J Microbiol. 2017; 65(4):433-442. DOI: 10.5604/17331331.1227669. View

12.

Martella V, Banyai K, Matthijnssens J, Buonavoglia C, Ciarlet M . Zoonotic aspects of rotaviruses. Vet Microbiol. 2009; 140(3-4):246-55. DOI: 10.1016/j.vetmic.2009.08.028. View

13.

Villena C, El-Senousy W, Abad F, Pinto R, Bosch A . Group A rotavirus in sewage samples from Barcelona and Cairo: emergence of unusual genotypes. Appl Environ Microbiol. 2003; 69(7):3919-23. PMC: 165171. DOI: 10.1128/AEM.69.7.3919-3923.2003. View

14.

Gouvea V, Santos N, Timenetsky M . Identification of bovine and porcine rotavirus G types by PCR. J Clin Microbiol. 1994; 32(5):1338-40. PMC: 263690. DOI: 10.1128/jcm.32.5.1338-1340.1994. View

15.

KATZENELSON E, Fattal B, Hostovesky T . Organic flocculation: an efficient second-step concentration method for the detection of viruses in tap water. Appl Environ Microbiol. 1976; 32(4):638-9. PMC: 170320. DOI: 10.1128/aem.32.4.638-639.1976. View

16.

Matthijnssens J, Ciarlet M, McDonald S, Attoui H, Banyai K, Brister J . Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol. 2011; 156(8):1397-413. PMC: 3398998. DOI: 10.1007/s00705-011-1006-z. View

17.

Keller R, Justino J, Cassini S . Assessment of water and seafood microbiology quality in a mangrove region in Vitória, Brazil. J Water Health. 2013; 11(3):573-80. DOI: 10.2166/wh.2013.245. View

18.

Trojnar E, Sachsenroder J, Twardziok S, Reetz J, Otto P, Johne R . Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses. J Gen Virol. 2012; 94(Pt 1):136-142. DOI: 10.1099/vir.0.047381-0. View

19.

Ortega O, El-Sayed N, Sanders J, Abd-Rabou Z, Antil L, Bresee J . Cost-benefit analysis of a rotavirus immunization program in the Arab Republic of Egypt. J Infect Dis. 2009; 200 Suppl 1:S92-8. DOI: 10.1086/605057. View

20.

Kamel A, Ali M, El-Nady H, Aho S, Pothier P, Belliot G . Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo. J Appl Microbiol. 2009; 108(5):1620-9. DOI: 10.1111/j.1365-2672.2009.04562.x. View