Simultaneous Detection of Multiple Respiratory Viruses Among SARS-CoV-2-Positive and Negative Patients by Multiplex TaqMan One-Step Real-Time PCR

Abstract

Background: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has clinical manifestations similar to other common respiratory viral infections. There are limited data on the frequency of viral respiratory coinfection among patients infected with SARS-CoV-2 in Iran. Objectives: This cross-sectional study investigated the prevalence of multiple respiratory viruses among SARS-CoV-2-positive and negative patients during the coronavirus disease 2019 (COVID-19) pandemic in Iran. Methods: We included oropharyngeal/nasopharyngeal swab specimens of patients suspected of COVID-19 from December 2020 to March 2021. A reliable multiplex TaqMan one-step real-time PCR method was employed to detect 17 viral respiratory pathogens simultaneously. Descriptive analyses were performed to characterize the specimens concerning age, gender, clinical manifestations, and underlying disease. Results: Multiple respiratory viruses with a frequency of 18.78% were detected in 197 studied patients. Human metapneumovirus was the most prevalent pathogen detected in both SARS-CoV-2-positive (n = 7, 7.7%) and negative (n = 7, 6.6%) patients. Moreover, the frequency rate of viral infection was almost the same in both SARS-CoV-2-positive (18.68%) and negative (18.86%) patients. Altogether, there were no differences in baseline demographic characteristics such as age, sex, clinical symptoms, and comorbidities between the two groups (P > 0.05). Conclusions: The data presented here expand our understanding of the epidemiology of multiple types of viral respiratory pathogens in suspected COVID-19 patients. Therefore, simultaneous screening of other viral respiratory pathogens will be helpful for clinicians and researchers interested in the control of viral respiratory tract infections.

The Circulation of Common Respiratory Viruses and Their Co-infection with Severe Acute Respiratory Syndrome Coronavirus 2 Before and After Coronavirus Disease of 2019 Vaccination

“…In line with our results, several studies reported a low rate of respiratory viral co-infections in COVID-19 patients. For example, Garcia-Vidal et al, Nowak et (8,9,15,(24)(25)(26)(27). Several reasons, such as viral interference in the established infection and competition among co-infecting viruses, as well as social distancing and wearing a mask in public and decreased circulation of other respiratory viruses, might lead to low rates of viral respiratory co-infections.…”

The prevalence of 17 common respiratory viruses in patients with respiratory illness but negative for COVID‐19: A cross‐sectional study

“…In a primary study conducted in Iran, using the HiTeq 17 Viro Respiratory pathogen One‐Step RT‐PCR Kit (Genova, Bonda Faravar, Bioluence, Tehran, Iran), from December 2020 to March 2021, a total of 197 cases were studied: 106 of these cases were reported as SARS‐CoV‐2 negative and 91 were identified as positive. They reported the pathogens and the relevant percentages as HMPV (7.1%), HCoV‐NL63 (4.06%), Flu B (1.52%), HCoV‐HKU1 (1.52%), HRSV (2.03%), HPiV (1.01%), HAdV (1.01%), and HBoV (0.5%) 7 . Interestingly, Veisi et al 7 found Flu B in 1.52% of their cases and no case of Flu A.…”

“…Moreover, the HiTeq 17 Viro Respiratory pathogen One‐Step RT‐PCR Kit (GeneovA), made in 2021 in Iran, was used in the present study; other studies have used this kit considering its appropriate sensitivity and specificity to identify various viral respiratory pathogens, including SARS‐CoV‐2, Flu A, Flu B, Flu A/H1N1, HCoV‐NL63, HCoV‐229E, HCoV‐HKU1, HCoV‐229E, HCoV‐OC43, HPiV‐1, ‐2, ‐3, HAdV, HBoV‐1, ‐2, ‐3, HMPV, and HRSV 7,26 …”

“…HiTeq 17 Viro Respiratory pathogen One‐Step RT‐PCR Kit (Genova, Bonda Faravar, Bioluence, Tehran, Iran) was used for respiratory virus detection 7 . Briefly, this multiplex real‐time PCR method identifies 17 respiratory viruses using a mixture of primers and probes for their conserved genomic regions.…”

“…HiTeq 17 Viro Respiratory pathogen One-Step RT-PCR Kit (Genova, Bonda Faravar, Bioluence, Tehran, Iran) was used for respiratory virus detection. 7 Briefly, this multiplex real-time PCR method identifies 17 respiratory viruses using a mixture of primers and probes for their conserved genomic regions. These viruses include SARS-CoV-2, Influenza A (Flu A), Influenza A/H1N1 (Flu A/H1N1), Influenza B (Flu B), human coronavirus (HCoV) HKU1, HCoV-NL63, HCoV-229E, human metapneumovirus (HMPV), human respiratory syncytial virus (HRSV), human bocavirus -1, -2, -3 (HBoV), human parainfluenza -1, -2, -3 (HPiV), human adenovirus (HAdV), HCoV-OC43, and reaction mix of this kit was prepared in three separate tubes (Supporting Information: Table 1).…”