Author(s): Hala A. Salah, Iman M. Aufi, Hula Y. Fadhil, Faisal G. Alhamdani


DOI: 10.5958/0974-360X.2020.00459.X   

Address: Hala A. Salah1, Iman M. Aufi2, Hula Y. Fadhil1*, Faisal G. Alhamdani2
1Biology Department, College of Science, University of Baghdad, Baghdad-Al-Jadiria, Iraq.
2Department of Virology, The National Central Public Health Laboratory (NPL), Ministry of Health, Baghdad, Iraq.
*Corresponding Author

Published In:   Volume - 13,      Issue - 6,     Year - 2020

This study aimed to award a local database for detection of human coronavirus (HCoV) species in patients with respiratory tract infections like influenza type A and a tuberculosis using Taqman reverse transcriptase real-time PCR (rRT-PCR) technique. A total of 389 respiratory samples was collected from individuals suffering from upper and/or lower respiratory tract diseases for testing of HCoV species (229E, OC43, NL63, HKU1 and MERS). RNA extracted and amplification with specific primers and probes. Result showed 35 (9%) positive sample and the probe assay associated with cycle number (Ct) was 33.98±0.97. It is interesting to note, the results pointed out 12/35 (34.29%) co–infected with the most frequently Flu A and the relative risk value represented 21.5 (95% Cl 4.9-93.9) of cohort influenza type A positive case. Moreover, the co-infection with pulmonary tuberculosis (TB) was 5/35 (14.29%) of HCoVs cases and the relative risk value 1.53 (95% Cl 0.68-3.45) of cohort TB positive cases. The percentage of a positive cases have a single HCoV species higher than multiple HCoV species with 31/35 (88.57%) and 4/35 (11.43%), respectively, and each viral species reported higher percentage as a single species than multiple. Also, the frequency of HCoV-229E and NL63 species consisted highest percentage 75% of four HCoV species with significant presence among Iraqi studying populations. Furthermore, the percentage of influenza virus A cases with HCoV infections were 7/12=58.33% with species 229E, while 60% of HCoV with TB infection appeared in NL63. In conclusion, the rRT-PCR based on Taqman observed the rapid and efficient detection of CoVs species with few copies number. This allows to be used for the diagnosis of CoVs along with other respiratory viruses in a multiplex assay to reduce processing time. Subsequent applied multiplex RT-PCR along with influenza and TB infections.

Cite this article:
Hala A. Salah, Iman M. Aufi, Hula Y. Fadhil, Faisal G. Alhamdani. Human Coronavirus Species and their correlation as co-infection detected by Fast Real-Time RT-PCR. Research J. Pharm. and Tech 2020; 13(6):2578-2584. doi: 10.5958/0974-360X.2020.00459.X

Hala A. Salah, Iman M. Aufi, Hula Y. Fadhil, Faisal G. Alhamdani. Human Coronavirus Species and their correlation as co-infection detected by Fast Real-Time RT-PCR. Research J. Pharm. and Tech 2020; 13(6):2578-2584. doi: 10.5958/0974-360X.2020.00459.X   Available on:

1.    Huynh J, Li S, Yount B, Smith A, Sturges L, Olsen JC, Nagel J, Johnson JB, Agnihothram S, Gates JE, Frieman M.B, Baric RS and  Donaldson EF. Evidence supporting a zoonotic origin of human coronavirus strain NL63. J Virol.86; 2012:12816–25.
2.    Drexler JF, Corman VM and Drosten C.  Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral Res.10; 12014:45–56.
3.    Gaunt ER, Hardie A, Claas EC, Simmonds P and Templeton KE. Epidemiology and clinical presentations of the four human coronaviruses 229E, HKU1, NL63, and OC43 detected over 3 years using a novel multiplex real-time PCR method. J Clin Microbiol.48; 2010:2940–2947.
4.    Zaki AM, van Boheemen S, Bestebroer TM, Osterhaus AD and  Fouchier RA. Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N Engl J of Med. 367; 2012:1814-1820.
5.    Lau SK, Lee P, Tsang AK, Yip CC, Tse H, Lee RA, So LY, Lau YL, Chan KH, Woo PC and  Yuen KY. Molecular epidemiology of human coronavirus OC43 reveals evolution of different genotypes over time and recent emergence of a novel genotype due to natural recombination. J Virol. 85(21); 2011:11325–37.
6.    Razuri H, Malecki M, Tinoco Y, Ortiz E, Guezala MC, Romero C, Estela A, Breña P, Morales ML, Reaves EJ, Gomez J, Uyeki TM, Widdowson MA, Azziz-Baumgartner E, Bausch DG, Schildgen V, Schildgen O and Montgomery JM.  Human Coronavirus-Associated Influenza-Like Illness in the Community Setting in Peru. Am J Trop Med Hyg.93; 2015:1038–40.
7.    Kuypers J, Wright N and Morrow R. Evaluation of quantitative and tybe- specific real-time RT-PCR assays for detection of respiratory syncytial virus in respiratory specimens fromchildren. J Clin Virol. 31; 2004: 123-129.
8.    Lu X, Whitaker B, Sakthivel SK, Kamili S, Rose LE,  Lowe L, Mohareb E,  Elassal EM, Al-sanouriT,  Haddadin A  and Erdman DD. Real-Time Reverse Transcription-PCR Assay Panel for Middle East Respiratory Syndrome Coronavirus. J Clin Microbiol.52(1); 2014: 67–75.
9.    Huh HJ, Kim JY, Kwon HJ, Yun SA, Lee MK, Ki CS, Lee NY and Kim JW. Performance Evaluation of the PowerChek MERS (upE & ORF1a) Real-Time PCR Kit for the Detection of Middle East Respiratory Syndrome Coronavirus RNA.Ann Lab Med.37(6); 2017:494-498.
10.    Centers for Disease Control and Prevention. Real-Time RT-PCR Assay for Non-Influenza Respiratory Viruses. 2012.
11.    Atyah NS, Fadhil HY,  Al-Hamadani FG, Auffi IM and Al-azzawi MA. Molecular detection of subfamily pneumovirinae among children with flu-like illness by using rt-pcr. Current Research in Microbiology and Biotechnology. 5(5); 2017: 1239-1244.
12.    Atyah NS, Fadhil HY,  Auffi IM  and  Al-Hamadani FG. First identification of Human Bocavirus (HBoV) in Iraqi children with respiratory complications. Journal of Pharmacy and Biological Sciences. 12(6); 2017:15-20.
13.    Khalaf RJ, Fadhil HY, Aufi IM and Namdar SA. Molecular diagnosis of human adenovirus in children with upper respiratory tract infections. Journal of Pharmacy and Biological Sciences. 12(3); 2017:09-13.
14.    Fadhil HY. Real-Time PCR Detection of Respiratory Syncytial virus (RSV) among adults with Pneumonia. Iraqi Journal of Science. 56(2C); 2015:1617-1621.
15.    Fadhil HY. Detection for respiratory syncytial virus rna among children with flu-like illness using molecular assay. International Journal of Current Research. 6 (11); 2014: 9455-9459.
16.    Zhang S, Tuo J, Huang X,  Zhu X, Zhang D,  Zhou K, Yuan L, Luo H, Zheng B, Yuen K,  Li M  and Cao K. Epidemiology characteristics of human coronaviruses in patients with espiratory infection symptoms and phylogenetic analysis of HCoV-OC43 during 2010-2015 in Guangzhou. PLoS One. 13(1); 2018: e0191789.
17.    Matoba Y, Aoki Y, Tanaka S, Yahagi K, Shimotai Y,  Matsuzaki Y, Itagaki T and Mizuta K. An Outbreak of Human Coronavirus OC43 during the 2014-2015 Influenza Season in Yamagata, Japan. Jpn J Infect Dis. 68(5); 2015:442-5.
18.    Chopra KK. SARS-TB co-infection in South East Asia. Indian J Tuberc.52; 2005:52.
19.    Liu W, Fontanet A, Zhang PH, Zhan L, Xin ZT, Tang F, Baril L, Cao WC. Pulmonary tuberculosis and SARS, China. Emerg Infect Dis. 12(4); 2006:707-9.
20.    Alfaraj SH,  Al-Tawfiq JA,  Altuwaijri TA and Memish ZA.  Middle East Respiratory Syndrome Coronavirus and Pulmonary Tuberculosis Coinfection: Implications for Infection Control. Ntervirology. 60; 2017:53–55.
21.    Piñana JL,  Madrid S, Pérez A, Hernández-Boluda JC, Giménez E, Terol MJ, Calabuig M,  Navarro D and Solano C. Epidemiologic and Clinical Characteristics of Coronavirus and Bocavirus Respiratory Infections after Allogeneic Stem Cell Transplantation: A Prospective Single-Center Study. Biol Blood Marrow Transplant. 24; 2018:563–570.
22.    Lepiller Q, Barth H, Lefebvre F, Herbrecht R, Lutz P, Kessler R, Fafi-Kremer S and Stoll-Keller F. High Incidence but Low Burden of Coronaviruses and Preferential Associations between Respiratory Viruses. Journal of Clinical Microbiology. 51(9); 2013:3039-46.
23.    Yip CC, Lam CS, Luk HK, Wong EY, Lee RA, So LY, Chan KH, Cheng VC, Yuen KY, Woo PC and Lau SK. A six-year descriptive epidemiological study of human coronavirus infections in hospitalized patients in Hong Kong. Virol Sin.31(1); 2016:41-8.
24.    Mackay IM, Arden KE, Speicher D, O'Neil NT, McErlean PK, Greer RM, Nissen MD and  Sloots TP. Co-circulation of four human coronaviruses (HCoVs) in Queensland children with acute respiratory tract illnesses in 2004. Viruses. 4; 2012:637–653.
25.    Vijgen L, Keyaerts E, Moës E, Maes P, Duson G and  Van Ranst M. Development of one-step, real-time, quantitative reverse transcriptase PCR assays for absolute quantitation of human coronaviruses OC43 and 229E. J Clin Microbiol. 43; 2005:5452–5456.
26.    Lau SK, Woo PC, Yip CC, Tse H, Tsoi HW, Cheng VC, Lee P, Tang BS, Cheung CH, Lee RA, So LY, Lau YL, Chan KH and Yuen KY. Coronavirus HKU1 and other coronavirus infections in Hong Kong. J Clin Microbiol. 44; 2006:2063–2071.
27.    Milano F, Campbell AP, Guthrie KA, Kuypers J, Englund JA, Corey L and  Boeckh M. Human rhinovirus and coronavirus detection among allogeneic hematopoietic stem cell transplantation recipients. Blood.115(10); 2010:2088-94.
28.    Hakki M, Rattray RM and Press RD. The clinical impact of coronavirus infection in patients with hematologic malignancies and hematopoietic stem cell transplant recipients. J Clin Virol. 68; 2015: 1-5. 28.
29.    Sipulwa LA, Ongus JR, Coldren RL and Bulimo WD. Molecular characterization of human coronaviruses and their circulation dynamics in Kenya, 2009-2012. Virol J. 1(13); 2016:18.
30.    Van Elden LJ, van Loon AM, van Alphen F, Hendriksen KA, Hoepelman AI, van Kraaij MG, Oosterheert JJ, Schipper P, Schuurman R and  Nijhuis M. Frequent detection of human coronaviruses in clinical specimens from patients with respiratory tract infection by use of a novel real-time reverse-transcriptase polymerase chain reaction. J Infect Dis.189(4); 2004:652-7.
31.    Owusu M, Annan A, Corman VM, Larbi R, Anti P, Drexler JF, Agbenyega O, Adu-Sarkodie Y and Drosten C. Human coronaviruses associated with upper respiratory tract infections in three rural areas of Ghana. PLoS One.9(7); 2014:e99782.
32.    Greenberg SB. Update on rhinovirus and coronavirus infections. Semin Resoir Crit Care Med. 32; 2011: 433–446.
33.    Kim KY, Han SY, Kim HS, Cheong HM, Kim SS and Kim DS. Human Coronavirus in the 2014 Winter Season as a Cause of Lower Respiratory Tract Infection. Yonsei Med J.58(1); 2017:174-179.
34.    Cabeça TK, Passos AM, Granato C and Bellei N. Human coronavirus occurrence in different populations of Sao Paulo: a comprehensive nine-year study using a pancoronavirus RT-PCR assay. Braz J Microbiol.44; 2013:335–339.
35.    Talbot HK, Shepherd BE, Crowe JE, Griffin MR, Edwards KM, Podsiad AB, Tollefson SJ, Wright PF and Williams JV. The pediatric burden of human coronaviruses evaluated for twenty years. Pediatr Infect Dis J.28(8); 2009:682-7.
36.    Al Johani S. and Hajeer AH. MERS-CoV diagnosis: An update. Journal of Infection and Public Health. 9(3); 2016: 216-219.
37.    Khalid M, Khan B, Al Rabiah F, Alismaili R, Saleemi S, Rehan-Khaliq AM, Weheba I, Al Abdely H, Halim M, Nadri QJ, Al Dalaan AM, Zeitouni M, Butt T and  Al Mutairy E. Middle Eastern Respiratory Syndrome Corona Virus (MERS CoV): case reports from a tertiary care hospital in Saudi Arabia. Ann Saudi Med. 34(5); 2014:396-400.
38.    Oh MD, Park WB, Park SW, Choe PG, Bang JH, Song KH, Kim ES, Kim HB, Kim NJ. Middle East respiratory syndrome: what we learned from the 2015 outbreak in the Republic of Korea. Korean J Intern Med.33(2); 2018:233-246.
39.    Aly M, Elrobh M, Alzayer M, Aljuhani S and  Balkhy H. Occurrence of the Middle East Respiratory Syndrome Coronavirus (MERS-CoV) across the Gulf Corporation Council countries: Four years update. Plos one.12(10); 2017: e0183850.
40.    Cho SY, Kang JM, Ha YE, Park GE, Lee JY, Ko JH, Lee JY, Kim JM, Kang CI, Jo IJ, Ryu JG, Choi JR, Kim S, Huh HJ, Ki CS, Kang ES, Peck KR, Dhong HJ, Song JH, Chung DR and  Kim YJ. MERS-CoV outbreak following a single patient exposure in an emergency room in South Korea: an epidemiological outbreak study. Lancet. 388(10048); 2016:994–1001.
41.    Park SH, Kim YS, Jung Y, Choi SY, Cho NH, Jeong HW, Heo JY, Yoon JH, Lee J, Cheon S and Sohn KM. Outbreaks of Middle East Respiratory Syndrome in Two Hospitals Initiated by a Single Patient in Daejeon, South Korea. Infect Chemother.48(2); 2016:99-107.
42.    Sha J, LiY, Chen X, Hu Y, Ren Y, Geng X, Zhang Z and Liu S. Fatality risks for nosocomial outbreaks of Middle East respiratory syndrome coronavirus in the Middle East and South Korea. Arch Virol.162(1); 2017:33-44.
43.    Al salihi SF and Alrodhan MA. phylogenetic Analysis of MERSCoV in Human and Camels in Iraq.International Journal of Pharmaceutical Research and Allied Sciences. 6(1); 2017:120-129.

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