Prevalence of Viral and Bacterial Co-Infections in SARS-CoV-2-Positive Individuals in Cyprus 2020–2022

The COVID-19 pandemic has had a profound impact on healthcare systems world-wide, with severe consequences on the global economy and society. The clinical presentation of SARS-CoV-2 infection varies widely, ranging from asymptomatic cases to severe disease and death. Coinfection with other respiratory pathogens in SARS-CoV-2-positive individuals may exacerbate symptom severity and lead to poorer clinical outcomes. Background/Objectives: This study is the first to investigate the prevalence of viral and bacterial co-infections in SARS-CoV-2-positive individuals in Cyprus. Methods: A total of 1,111 SARS-CoV-2-positive nasopharyngeal swab samples were analysed for the presence of 18 viral and 3 bacterial respiratory pathogens. Re-sults: Of these, 51 samples (4.6%) were found to have at least one additional respira-tory pathogen. The most frequently detected viruses were Rhinovirus/Enterovirus (n = 28; 2.5%) and Adenovirus (n = 8; 0.7%), while the bacterial pathogens identified were Legionella pneumophila (n = 1; 0.1%) and Bordetella pertussis (n = 1; 0.1%). The highest proportion of co-infections was observed in the youngest age group (<10 years), where 52.9% of co-infections were identified, followed by the 30–39 age group, which ac-counted for 15.7% of cases. Among single respiratory virus co-infections, Rhinovi-rus/Enterovirus (27.5%) and Adenovirus (13.7%) were the most frequently detected in the <10 age group, followed by RSV (3.9%), Bocavirus, Influenza B, HMPV A+B, and Coronavirus NL63 (each at 2%). Conclusions: The current study underscores the im-portance of detecting co-infections in SARS-CoV-2-positive individuals, as this could have significant implications for therapeutic management. Early identification of coinfecting pathogens may guide targeted treatment strategies, reduce complications, and improve overall clinical outcomes.