Human Coronavirus Species and their correlation as co-infection detected by Fast Real-Time RT-PCR

Abstract

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 0.683.45) 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.