Evaluation of the Respiratory Viral Panel PCR Test Results Before and After COVID-19 Pandemic


ALP A., Tasci O., ERGİN M. A. , Koseoglu Eser O.

MIKROBIYOLOJI BULTENI, vol.56, no.4, pp.667-681, 2022 (SCI-Expanded) identifier

  • Publication Type: Article / Article
  • Volume: 56 Issue: 4
  • Publication Date: 2022
  • Doi Number: 10.5578/mb.20229605
  • Journal Name: MIKROBIYOLOJI BULTENI
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, BIOSIS, EMBASE, TR DİZİN (ULAKBİM)
  • Page Numbers: pp.667-681
  • Keywords: Respiratory virus, SARS-CoV-2, COVID-19, coinfection, multiplex real-time PCR, DIAGNOSIS, VIRUSES, INFECTIONS, SAMPLES
  • Hacettepe University Affiliated: Yes

Abstract

During the ongoing Coronavirus disease-2019 (COVID-19) pandemic, infections caused by other respiratory viruses continue to be seen and constitute an important health problem. In this study, it was aimed to evaluate the frequencies of respiratory tract viruses detected by respiratory tract virus panel (Allplex Respiratory Panel, Seegene, South Korea) multiplex real-time PCR test in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) pre-pandemic period, and in the first and second year of the pan- demic. The distribution of viral agents between these three periods was also investigated. In addition, it was planned to investigate the frequency of coinfection with SARS-CoV-2 and other respiratory tract viruses during the pandemic. When the sum of the three periods were evaluated together, it was obser- ved that at least one respiratory tract virus was detected in 13 802 (32.7%) of 42 174 samples. While at least one respiratory tract virus was detected in 8740 (54.6%) of 16 002 samples in the pre-pandemic period, at least one respiratory tract virus was detected in 1638 (9.4%) of 17 510 samples in the first year of the pandemic, and in 3424 (39.5%) of 8662 samples in the second year of the pandemic. In the first year of the pandemic, a statistically significant difference was observed that the number of viruses detected decreased due to closure measures and the use of personal protective equipment (p< 0.001). It was determined that the frequency of the detection of respiratory tract viruses other than SARS-CoV-2 started to increase again and a statistically significant difference occurred in the third period when vac- cination started and the transition to normalization began by gradually loosening the closure measures (p< 0.001). Rhinovirus was the most frequently detected virus in all three periods of the study (First peri- od: 16.5%; second period: 5.9%; third period: 16.5). More than one respiratory tract virus was detected simultaneously in 2061 (14.9%) of 13 802 samples, in which at least one respiratory tract virus was detected within the scope of the study. Rhinovirus (7.3%) took the first place among the viruses found in coinfection. In the second and third periods covering the pandemic period, it was observed that the SARS-CoV-2 PCR result was also positive in 177 (4.2%) of 4219 samples whose respiratory tract virus panel PCR results were positive and simultaneously had a SARS-CoV-2 PCR test request. Therefore, it was concluded that SARS-CoV-2 coinfection can be observed in the same patient with other respiratory tract viruses in respiratory tract samples. The addition of SARS-CoV-2 to the respiratory tract virus multiplex PCR panels currently in use will enable faster detection of such coinfections. It is thought that both the incidence of respiratory tract virus infections other than SARS-CoV-2 and the rate of coinfection with other respiratory tract viruses in SARS-CoV-2 infection may increase with the relaxation of the measures taken for the control of the pandemic. For this reason, the detection of viruses that cause respiratory tract infections from clinical samples with reliable and rapid methods will ensure the measures to be taken to protect public health without delay and thus contribute to the prevention of the spread of infections.