Genotyping of Rotaviruses in River Nile in Giza, Egypt
,
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.
1. Onda K, LoBuglio J, Bartram J (2012). Global access to safe water: Accounting for water quality andthe resulting impact on MDG progress. Int J Environ Res Public Health, 9: 880–894.
2. Tate JE, Burton AH, Boschi-Pinto C et al (2012). 2008 estimate of worldwide rota-virus-associated mortality in children younger than 5 years before the introduc-tion of universal rotavirus vaccination programs: a systematic review and meta-analysis. Lancet Infect Dis, 12:136–141
3. Khoury H, Ogilvie I, El Khoury AC et al(2011). Burden of rotavirus gastroenteri-tis in the Middle Eastern and North Afri-can pediatric population. BMC Infect Dis, 11:9.
4. UNICEF. Children in Egypt: a statistical di-gest. Chapter 3: Child and maternal mor-tality. 2015. https://www.unicef.org/eg_UNICEF-2015-Children-in-Egypt-Statistical-Digest(3).pdf
5. Matthijnssens J, Ciarlet M, McDonald SM et al(2011). Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol, 156: 1397–1413.
6. Trojnar E, Sachsenroder J, Twardziok S et al(2013). Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses. J Gen Virol, 94: 136–142.
7. Martella V, Banyai K, Matthijnssens J, Buonavoglia C, Ciarlet M (2010). Zoono-tic aspects of rotaviruses. Vet Microbiol, 140: 246–255.
8. Gentsch JR, Laird AR, Bielfelt B et al(2005).Serotype Diversity and Reas-sortment between Human and Animal Rotavirus Strains: Implications for Rota-virus Vaccine Programs. J Infect Dis, S146–159.
9. Matson DO, Abdel-Messih IA, Schlett CD et al (2010). RVA Genotypes among hospitalized children in Egypt, 2000–2002. J Infect Dis, 202(S1): S263–265.
10. Ortega O, El-Sayed N, Sanders JW et al(2009). Cost-benefit analysis of a RVA immunization program in the Arab Re-public of Egypt. J Infect Dis, 200: S92–98.
11. Saudy N, Elshabrawy WO et al(2017). Gen-otyping and clinicoepidemiological char-acterization of rotavirus acute gastroenter-itis in Egyptian children. Polish J microbial, 65, 4:433–442.
12. Kamel AH, Ali MA et al(2010). Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo. J Appl Microb, 108: 1620–1629.
13. Shoeiba, AR, Hull JJ, Jiang B (2015). Rota-virus G and P types in children with acute diarrhea in Cairo, Egypt, 2011-2012. J Egypt Public Health Assoc, 90:121–124.
14. Villena C, El-Senousy WM, Abad FX et al(2003). Group A rotavirus in sewage samples from Barcelona and Cairo: emergence of unusual genotypes. Appl Environ Microbiol, 69: 3919–3923.
15. Rose JB, Singh SN, Gerba CP, Kelley LM (1984). Comparison of microporous fil-ters for concentration of viruses from wastewater. Appl Environ Microbiol, 47:989–992.
16. Katzenelson E, Fattal B, Hostovesky T (1976). Organic flocculation: an efficient second-step concentration method for the detection of viruses in tap water. Appl Environ Microbiol, 32:838–839.
17. Jim Gray and Miren Iturriza-Gómara Rota-viruses (chapter). Stephenson JR, Warnes A. (Eds.). Diagnostic Virology Protocols (book) in molecular biology. Springer Science Ste-phenson JR, Warnes A. (Eds.). Springer Science vol. 665. Pp. 325-355.
18. Gouvea V, Santos N, Timenetsky MC (1994). Identification of bovine and por-cine rotavirus G types by PCR. J Clin Mi-crobiol, 32:1338–1340.
19. Gouvea V, Santos N, M., Timenetsky MC (1994). VP4 typing of bovine and porcine group A rotavirus by PCR. J Clin Microbiol, 32:1333–1337.
20. Meyer RK, David DK. A Minitab Guide to Statistics (3rd Ed.). Upper Saddle River, NJ: Prentice-Hall Publishing; 2004.
21. Petrinca AR, Donia D, Pierangeli A et al (2009). Presence and environmental circu-lation of enteric viruses in three different wastewater treatment plants. J Appl Micro-biol, 106: 1608–1617.
22. El-Senousy WM, Barakat AB et al(2013). Molecular Epidemiology of Human Ade-noviruses and Rotaviruses as Candidate Viral Indicators in the Egyptian Sewage and Water Samples. World Appl Sci J, 27: 1235-1247
23. El-Senousy WM, Ragab AME, Handak EMA (2015). Prevalence of Rotaviruses Groups A and C in Egyptian Children and Aquatic Environment. Food Environ Virol, 7:132–141.
24. Kittigul L, Panjangampatthana A, Rupprom K, Pombubpa K (2014).Genetic Diversity of Rotavirus Strains Circulating in Envi-ronmental Water and Bivalve Shellfish in Thailand.Int J Environ Res Public Health.11: 1299-1311.
25. Katukiza AY, Temanu H, Chung JW et al (2013). Genomic copy concentrations of selected waterborne viruses in a slum en-vironment in Kampala, Uganda. J Water Health, 11: 358–370.
26. Keller R, Justino JF, Cassini ST (2013). As-sessment of water and seafood microbi-ology quality in a mangrove region in Vi-tória, Brazil. J Water Health, 11: 573-580.
27. Räsänen S, Lappalainen S, Kaikkonen S et al (2010). Mixed viral infections causing acute gastroenteritis in children in a wa-terborne outbreak. Epidemiol Infect, 138: 1227–1234.
28. Koroglu M, Yakupogullari Y, Otlu B et al (2011). A waterborne outbreak of epi-demic diarrhea due to group A rotavirus in Malatya, Turkey. New Microbiol, 34: 17–24.
29. Mellou K, Katsioulis A, Potamiti-Komi M et al (2014). A large waterborne gastroenteri-tis outbreak in central Greece, March 2012: Challenges for the investigation and management. Epidemiol Infect, 142: 40–50.
30. Araújo IT, Ferreira MS, Fialho AM et al (2001). Rotavirus genotypes P[4]G9, P[6]G9, and P[8]G9 in hospitalized chil-dren with acute gastroenteritis in Rio de Janeiro, Brazil. J Clin Microbiol, 39(5):1999-2001.
31. Jain V, Das BK, Bhan MK, et al (2001). Great diversity of group A rotavirus strains and high prevalence of mixed ro-tavirus infections in India. J Clin Microbiol, 39(10):3524-9.
32. Fang ZY, Yang H, Qi J, Zhang J, Sun LW et al (2002). Diversity of rotavirus strains among children with acute diarrhea in China: 1998-2000 surveillance study. J Clin Microbiol, 40(5):1875-8.
33. Chaimongkol N, Khamrin P, Malasao R et al(2012). Genotypic linkages of gene segments of rotaviruses circulating in pe-diatric patients with acute gastroenteritis in Thailand. Infect Genet Evol, 12: 1381–1391.
34. Afrad MH, Hassan Z, Farjana S et al (2013). Changing profile of rotavirus genotypes in Bangladesh, 2006–2012. BMC Infect Dis, 13: 313-320.
2. Tate JE, Burton AH, Boschi-Pinto C et al (2012). 2008 estimate of worldwide rota-virus-associated mortality in children younger than 5 years before the introduc-tion of universal rotavirus vaccination programs: a systematic review and meta-analysis. Lancet Infect Dis, 12:136–141
3. Khoury H, Ogilvie I, El Khoury AC et al(2011). Burden of rotavirus gastroenteri-tis in the Middle Eastern and North Afri-can pediatric population. BMC Infect Dis, 11:9.
4. UNICEF. Children in Egypt: a statistical di-gest. Chapter 3: Child and maternal mor-tality. 2015. https://www.unicef.org/eg_UNICEF-2015-Children-in-Egypt-Statistical-Digest(3).pdf
5. Matthijnssens J, Ciarlet M, McDonald SM et al(2011). Uniformity of rotavirus strain nomenclature proposed by the Rotavirus Classification Working Group (RCWG). Arch Virol, 156: 1397–1413.
6. Trojnar E, Sachsenroder J, Twardziok S et al(2013). Identification of an avian group A rotavirus containing a novel VP4 gene with a close relationship to those of mammalian rotaviruses. J Gen Virol, 94: 136–142.
7. Martella V, Banyai K, Matthijnssens J, Buonavoglia C, Ciarlet M (2010). Zoono-tic aspects of rotaviruses. Vet Microbiol, 140: 246–255.
8. Gentsch JR, Laird AR, Bielfelt B et al(2005).Serotype Diversity and Reas-sortment between Human and Animal Rotavirus Strains: Implications for Rota-virus Vaccine Programs. J Infect Dis, S146–159.
9. Matson DO, Abdel-Messih IA, Schlett CD et al (2010). RVA Genotypes among hospitalized children in Egypt, 2000–2002. J Infect Dis, 202(S1): S263–265.
10. Ortega O, El-Sayed N, Sanders JW et al(2009). Cost-benefit analysis of a RVA immunization program in the Arab Re-public of Egypt. J Infect Dis, 200: S92–98.
11. Saudy N, Elshabrawy WO et al(2017). Gen-otyping and clinicoepidemiological char-acterization of rotavirus acute gastroenter-itis in Egyptian children. Polish J microbial, 65, 4:433–442.
12. Kamel AH, Ali MA et al(2010). Evidence of the co-circulation of enteric viruses in sewage and in the population of Greater Cairo. J Appl Microb, 108: 1620–1629.
13. Shoeiba, AR, Hull JJ, Jiang B (2015). Rota-virus G and P types in children with acute diarrhea in Cairo, Egypt, 2011-2012. J Egypt Public Health Assoc, 90:121–124.
14. Villena C, El-Senousy WM, Abad FX et al(2003). Group A rotavirus in sewage samples from Barcelona and Cairo: emergence of unusual genotypes. Appl Environ Microbiol, 69: 3919–3923.
15. Rose JB, Singh SN, Gerba CP, Kelley LM (1984). Comparison of microporous fil-ters for concentration of viruses from wastewater. Appl Environ Microbiol, 47:989–992.
16. Katzenelson E, Fattal B, Hostovesky T (1976). Organic flocculation: an efficient second-step concentration method for the detection of viruses in tap water. Appl Environ Microbiol, 32:838–839.
17. Jim Gray and Miren Iturriza-Gómara Rota-viruses (chapter). Stephenson JR, Warnes A. (Eds.). Diagnostic Virology Protocols (book) in molecular biology. Springer Science Ste-phenson JR, Warnes A. (Eds.). Springer Science vol. 665. Pp. 325-355.
18. Gouvea V, Santos N, Timenetsky MC (1994). Identification of bovine and por-cine rotavirus G types by PCR. J Clin Mi-crobiol, 32:1338–1340.
19. Gouvea V, Santos N, M., Timenetsky MC (1994). VP4 typing of bovine and porcine group A rotavirus by PCR. J Clin Microbiol, 32:1333–1337.
20. Meyer RK, David DK. A Minitab Guide to Statistics (3rd Ed.). Upper Saddle River, NJ: Prentice-Hall Publishing; 2004.
21. Petrinca AR, Donia D, Pierangeli A et al (2009). Presence and environmental circu-lation of enteric viruses in three different wastewater treatment plants. J Appl Micro-biol, 106: 1608–1617.
22. El-Senousy WM, Barakat AB et al(2013). Molecular Epidemiology of Human Ade-noviruses and Rotaviruses as Candidate Viral Indicators in the Egyptian Sewage and Water Samples. World Appl Sci J, 27: 1235-1247
23. El-Senousy WM, Ragab AME, Handak EMA (2015). Prevalence of Rotaviruses Groups A and C in Egyptian Children and Aquatic Environment. Food Environ Virol, 7:132–141.
24. Kittigul L, Panjangampatthana A, Rupprom K, Pombubpa K (2014).Genetic Diversity of Rotavirus Strains Circulating in Envi-ronmental Water and Bivalve Shellfish in Thailand.Int J Environ Res Public Health.11: 1299-1311.
25. Katukiza AY, Temanu H, Chung JW et al (2013). Genomic copy concentrations of selected waterborne viruses in a slum en-vironment in Kampala, Uganda. J Water Health, 11: 358–370.
26. Keller R, Justino JF, Cassini ST (2013). As-sessment of water and seafood microbi-ology quality in a mangrove region in Vi-tória, Brazil. J Water Health, 11: 573-580.
27. Räsänen S, Lappalainen S, Kaikkonen S et al (2010). Mixed viral infections causing acute gastroenteritis in children in a wa-terborne outbreak. Epidemiol Infect, 138: 1227–1234.
28. Koroglu M, Yakupogullari Y, Otlu B et al (2011). A waterborne outbreak of epi-demic diarrhea due to group A rotavirus in Malatya, Turkey. New Microbiol, 34: 17–24.
29. Mellou K, Katsioulis A, Potamiti-Komi M et al (2014). A large waterborne gastroenteri-tis outbreak in central Greece, March 2012: Challenges for the investigation and management. Epidemiol Infect, 142: 40–50.
30. Araújo IT, Ferreira MS, Fialho AM et al (2001). Rotavirus genotypes P[4]G9, P[6]G9, and P[8]G9 in hospitalized chil-dren with acute gastroenteritis in Rio de Janeiro, Brazil. J Clin Microbiol, 39(5):1999-2001.
31. Jain V, Das BK, Bhan MK, et al (2001). Great diversity of group A rotavirus strains and high prevalence of mixed ro-tavirus infections in India. J Clin Microbiol, 39(10):3524-9.
32. Fang ZY, Yang H, Qi J, Zhang J, Sun LW et al (2002). Diversity of rotavirus strains among children with acute diarrhea in China: 1998-2000 surveillance study. J Clin Microbiol, 40(5):1875-8.
33. Chaimongkol N, Khamrin P, Malasao R et al(2012). Genotypic linkages of gene segments of rotaviruses circulating in pe-diatric patients with acute gastroenteritis in Thailand. Infect Genet Evol, 12: 1381–1391.
34. Afrad MH, Hassan Z, Farjana S et al (2013). Changing profile of rotavirus genotypes in Bangladesh, 2006–2012. BMC Infect Dis, 13: 313-320.
| Files | ||
| Issue | Vol 49 No 1 (2020) | |
| Section | Short Communication(s) | |
| DOI | https://doi.org/10.18502/ijph.v49i1.3065 | |
| Keywords | ||
| Rotavirus Genotype Water River Nile Egypt | ||
| Rights and permissions | |
|
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
How to Cite
1.
RIZK NM, ALLAYEH AK. Genotyping of Rotaviruses in River Nile in Giza, Egypt. Iran J Public Health. 2020;49(1):173-180.
