WHOLE-GENOME SEQUENCING ANALYSIS OF HUMAN BOCAVIRUS DETECTED IN CHILDREN SUFFERING FROM RESPIRATORY TRACT INFECTION IN BASRAH CITY, SOUTH IRAQ
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Keywords
HBOV, ARTI, genome, sequencing
Abstract
In 2005, Allander and colleagues at Karolinska Institute found the human bocavirus (HBoV) in a collection of nasopharyngeal aspirates. There are four human bocavirus species, HBoV1-4 the three species HBoV2, HBoV3, and HBoV4 were caused gastroenteritis and mainly found in stool samples. While HBoV1 causes upper and lower respiratory tract infections (RTI). The HBoV genome is arranged into three open reading structures, ORF1 at the 5' end, ORF2 at the 3' end, and ORF3 at the 3' end, encoding two protein structures, VP1 and VP2. Two hundred oropharyngeal swab specimens were collected from hospitalized children under 5 years old who have been suffering from acute respiratory tract infection (ARTI) from Basrah Maternity and Children Hospital in Basrah city. In the period from December 2020 to December 2021. The human bocavirus was identified by Multiplex OneStep. In a total of 200 tested samples, HBoV was detected in 28 (14%) samples. Analysis of the whole sequence of strain NHAB1 (OP593329) revealed that this strain is similar to HBoV strains at 98.14–98.72%. The allusion strain HZ1303 (KP710210) discovered in China had the highest identical sequences (98.72%). The current study isolates clustered with KP710210 (HBoV type I China isolation). The nucleotide sequences of these genes (NS1, NP1, VP1, and VP2) were translated into the corresponding amino acid. It was discovered that the NS1 aa contained three aa substitutions: at position aa106, glycine (Gly) changed to arginine (Arg). Also, in position aa228 the cysteine (Cys) substituted to glycine (Gly) and in position aa229 the asparagine (Asp) substituted with glutamine (Glu). One aa alteration was found in the NP1 aa sequences at position aa79, where serine (Ser) was changed to asparagine (Asn). While, Among VP1 and VP2 aa there was not substitution detected.
References
2. Abdel-Moneim, A. S., Kamel, M. M., Hamed, D. H., Hassan, S. S., Soliman, M. S., Al-Quraishy, S. A., & El Kholy, A. A. (2016). A novel primer set for improved direct gene sequencing of human bocavirus genotype-1 from clinical samples. Journal of virological methods, 228, 108-113.
3. Abozahra, R., Abdelhamid, S. M., Khairy, K., & Baraka, K. (2020). Detection and phylogenetic analysis of Human bocavirus in children diagnosed with acute respiratory tract infection. Journal of Medical Microbiology, 69(9), 1197-1202.
4. Allander, T., Tammi, M. T., Eriksson, M., Bjerkner, A., Tiveljung-Lindell, A., & Andersson, B. (2005). Cloning of a human parvovirus by molecular screening of respiratory tract samples. Proceedings of the National Academy of Sciences, 102(36), 12891-12896.
5. Al-Shuwaikh, A.M. (2021). Human bocavirus in children with respiratory tract infection: Molecular and serological detection. The Scientific Journal of King Faisal University: Basic and Applied Sciences, 22(2), 71–5. DOI:10.37575/b/med/210054
6. Atyah, N. S., Fadhil, H. Y., Auffi, I. M., & Al-Hamadani, F. G. (2017). First identification of human bocavirus (HBoV) in Iraqi children with respiratory complications. J. Pharmacy and Biological Sciences, 12(6), 15-20.
7. Bastien, N., Brandt, K., Dust, K., Ward, D., & Li, Y. (2006). Human bocavirus infection, Canada. Emerging infectious diseases, 12(5), 848.
8. Bharaj, P., Sullender, W. M., Kabra, S. K., & Broor, S. (2010). Human bocavirus infection in children with acute respiratory tract infection in India. Journal of medical virology, 82(5), 812-816.
9. Dawood, F. S., Iuliano, A. D., Reed, C., Meltzer, M. I., Shay, D. K., Cheng, P. Y., ... & Widdowson, M. A. (2012). Estimated global mortality associated with the first 12 months of 2009 pandemic influenza A H1N1 virus circulation: a modelling study. The Lancet infectious diseases, 12(9), 687-695.
10. Hasan DA, Hussein AA, et al (2020): Phylogenetic analysis of human bocavirus isolated from children with lower respiratory tract infections in Baghdad, Iraq, Ann Trop Med & Pub Health; 23:S418. DOI: http://doi.org/10.36295/ASRO.2020.23132
11. Hosseininasab, A., Mollaei, H. R., & Karimi, Z. (2021). Prevalence of Human Bocavirus in Children Under 5 Years with Upper and Lower Respiratory Infections in Southeastern Iran. Archives of Pediatric Infectious Diseases, (In Press).
12. Huang, Q., Deng, X., Yan, Z., Cheng, F., Luo, Y., Shen, W., Lei-Butters, D.C., Chen, A.Y., Li, Y., Tang, L., Soderlund-Venermo, M., Engelhardt, G.F., Qiu, J. (2012). Establishment of a reverse genetics system for studying human bocavirus in human airway epithelia. PLoS. Pathogens, 8(8), e1002899.
13. Hussein, R. A. (2018). Patterns of Documenting Patients' Medical Records and Antibiotic Use for Cases with Acute Respiratory Infection in Basrah hospitals. University of Thi-Qar Journal of Medicine, 15(1), 1-11.
14. Kang, L. H., Won, Y. J., Lee, A. R., Lee, S. G., Cho, H. G., Park, Y. J., ... & Paik, S. Y. (2018). Whole-genome sequencing analysis of human bocavirus detected in South Korea. Epidemiology & Infection, 146(7), 839-847.
15. Kenmoe, S., Vernet, M. A., Njankouo-Ripa, M., Penlap, V. B., Vabret, A., & Njouom, R. (2017). Phylogenic analysis of human bocavirus detected in children with acute respiratory infection in Yaounde, Cameroon. BMC Research Notes, 10, 1-5.
16. Koseki, N., Teramoto, S., Kaiho, M., Gomi-Endo, R., Yoshioka, M., Takahashi, Y., ... & Ishiguro, N. (2012). Detection of human bocaviruses 1 to 4 from nasopharyngeal swab samples collected from patients with respiratory tract infections. Journal of clinical microbiology, 50(6), 2118-2121.
17. Maggi, F., Andreoli, E., Pifferi, M., Meschi, S., Rocchi, J., & Bendinelli, M. (2007). Human bocavirus in Italian patients with respiratory diseases. Journal of Clinical Virology, 38(4), 321-325.
18. Mohammed-Jawad, N. K., Abdulrahman, N. M., Emad, A., & Jumaa, S. (2020). Assessment of dosing errors in pediatric patients prescriptions in Basra city. Arch. Pharm. Pract, 11(1), 73-6.
19. Nadji, S. A., Poos-Ashkan, L., Khalilzadeh, S., Baghaie, N., Shiraghaei, M. J., Hassanzad, M., & Bolursaz, M. R. (2010). Phylogenetic analysis of human bocavirus isolated from children with acute respiratory illnesses and gastroenteritis in Iran. Scandinavian journal of infectious diseases, 42(8), 598-603.
20. Prabantu, V. M., Naveenkumar, N., & Srinivasan, N. (2021). Influence of disease-causing mutations on protein structural networks. Frontiers in Molecular Biosciences, 7, 620554.
21. Principi, N., Piralla, A., Zampiero, A., Bianchini, S., Umbrello, G., Scala, A., ... & Esposito, S. (2015). Bocavirus infection in otherwise healthy children with respiratory disease. PLoS One, 10(8), e0135640.
22. Thurman, K. A., Walter, N. D., Schwartz, S. B., Mitchell, S. L., Dillon, M. T., Baughman, A. L., ... & Winchell, J. M. (2009). Comparison of laboratory diagnostic procedures for detection of Mycoplasma pneumoniae in community outbreaks. Clinical infectious diseases, 48(9), 1244-1249.
23. Wang, Y., Li, Y., Liu, J., Zhao, Y., Xie, Z., Shen, J., & Tan, W. (2016). Genetic characterization of human bocavirus among children with severe acute respiratory infection in China. Journal of Infection, 73(2), 155-163.
24. Watanabe, A.S.A., Luchs, A. and Leal, E. (2018). Complete genome sequences of six human bocavirus strains from patients with acute gastroenteritis in the north region of Brazil. Viruses, 6(17), e00235–18. DOI: 10.1128/genomeA.00235-18
25. Yaseen, Z. T., Khudair, M. K., Naseef, A. S., & Alezzi, J. I. (2020). Detection of Human Bocavirus in Children Suffering from Respiratory Tract Infection in Diyala Province. Diyala Journal of Medicine, 18(2), 121-129.
26. Zhou, L., Zheng, S., Xiao, Q., Ren, L., Xie, X., Luo, J., ... & Liu, E. (2014). Single detection of human bocavirus 1 with a high viral load in severe respiratory tract infections in previously healthy children. BMC infectious diseases, 14(1), 1-8.
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Noora Khudhur Abdulqader
Department of Biology, College of Science, University of Basrah, Basrah, Iraq
Hazim Talib Thwiny
Al-Zahraa College of Medicine, University of Basrah, Basrah, Iraq
Aida A. Manthar
College of Medicine, University of Basrah, Basrah, Iraq