Molecular detection of endemic coronaviruses and enterovirus D68 in respiratory samples from 2016 in Panama: a retrospective study

In 2016, Panama’s Surveillance Program for Influenza and Other Respiratory Viruses received 4041 samples with suspected viral respiratory infection, of which 68.78% tested positive on the respiratory viral panel, while the remaining 31.22% resulted in no etiological diagnosis. Given the need to determine which other viruses could cause these respiratory infections, a retrospective search for endemic coronaviruses and Enterovirus D68 was conducted, with the primary objective of detecting them in negative samples from that year. One hundred and twenty-seven nasopharyngeal swab samples were retrospectively selected, all of which had been previously tested using a routine respiratory viral panel for pandemic Influenza viruses, Respiratory Syncytial Virus (RSV), Human Metapneumovirus (hMPV), Parainfluenza viruses (PIV-1, PIV-2, PIV-3), Adenovirus (AdV), and Rhinovirus (RV). Of these, 70% were negative and 30% positive for at least one respiratory virus, and were subsequently classified by age group, clinical outcome and geographic location. Nucleic acids were extracted using automated equipment and amplified by Reverse Transcription Quantitative Polymerase Chain Reaction (RT-qPCR). The human RNase P gene was used as an internal control. Samples and controls were considered positive with a Ct value ≤ 35 cycles. The statistical analysis was performed using Pearson’s chi-square, considering a p value < 0.05 as statistically significant. The human coronavirus 229E (HCoV-229E) (n = 3), human coranvirus OC-43 (HCoV-OC43) (n = 3) and EV-D68 (n = 17) viruses were detected, presenting viral co-detections between HCoV-229E/pandemic Influenza A/H1, HCoV-OC43/Parainfluenza type 1, Enterovirus D68/Rhinovirus, Enterovirus D68/Respiratory Syncytial Virus and Enterovirus D68/Parainfluenza type 3. Overall, 78.26% (n = 18/23) of the cases were hospitalized patients and 21.74% (n = 5/23) were outpatients. Regarding age, 52.17% (n = 12/23) of the cases corresponded to children under 5 years old, 13.04% (n = 3/23) to patients between 5 and 18 years old, and 34.78% (n = 8/23) to adults over 18 years old. The circulation of HCoV-229E, HCoV-OC43, and EV-D68 was confirmed, causing both single respiratory infections and co-detections with other viruses from the routine diagnostic panel. This is why it is crucial to expand our knowledge of the epidemiology of respiratory viruses that are not currently part of routine surveillance systems, but which could be contributing significantly to the burden of disease in the population.