Prevalence, clinical characteristics and pattern of distribution of seasonal corona virus associated acute respiratory tract infections among adults and children in the Central Province of Sri Lanka from January 2020 to October 2022

Human coronaviruses (hCoVs) are frequently detected in nasopharyngeal samples from patients with acute respiratory tract infections (ARTIs). Interest in hCoVs increased following the severe acute respiratory syndrome coronavirus (SARS-CoV) outbreak in 2002. However, epidemiological data on seasonal coronaviruses (sCoVs) remain incomplete, particularly in settings where these viruses are not routinely tested in standard respiratory diagnostic panels. Limited surveillance of sCoVs may hinder early detection of emerging CoVs and pandemic preparedness. In the current study, a total of 1062 respiratory samples from patients with ARTIs were tested to detect 22 respiratory pathogens including sCoVs using a real time reverse transcription multiplex polymerase chain reaction (real time RT-multiplex PCR) from January 2020 to October 2022. Respiratory pathogens were identified in 51.03% patients with the detection rate of 7% for sCoVs. Of the sCoV positive patients, 36 were hCoV-NL63/HKU1 infections; 29 were hCoV-229E infections and 9 were hCoV-OC43 infections. Fever, cough and sore throat were the most common symptoms detected in all three sCoV infections. hCoV-229E and hCoV-NL63/HKU1 were not detected in 2020. A major peak of hCoV-229E infection was noted in April 2021 with detection from January 2021 to July 2022. Major peaks of hCoV-NL63/HKU1 infections were noted in April 2021 and 2022. The least prevalent sCoV in the study was hCoV-OC43, which was detected in January to March in 2020 and the virus was not detected in 2021 and two hCoV-OC43 infections were detected in 2022. Based on the present study findings, prevalence of sCoV infections among patients with ARTI was 6.96% with hCoV-NL63/HKU1 predominance. sCoVs were detected year-round, with peak incidence noted in January and February of 2021/2022. sCoVs distribution fluctuated along with SARS-CoV-2 infections during the pandemic. Implementing a national sCoV surveillance system could enhance early detection and monitoring of sCoVs, aiding the tracking of emerging hCoVs.