Co-Infection with respiratory viruses among critically-ill SARS-CoV2 patients in a tertiary hospital in Egypt: Incidence and effect on patients outcome

Background: Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection could be associated with other co/super-infections that worsen the outcome. In our hospital, the burden of viral co-infections with SARS-CoV-2 is unknown. We aimed to identify the lower respiratory tract viral pathogens causing co-infections among SARS-CoV-2 patients, and to elucidate their outcome. Subjects and Methods: We enrolled 147 patients with SARS-CoV-2 infection. Lower respiratory viral co-infection was identified in non-repetitive respiratory specimens by Biofire FilmArray Pneumonia Panel. Culture and Vitek-2 were used to identify bacterial and/or fungal super-infections in co-infected patients whose outcome was evaluated. Results: Of 147 enrolled patients, 29 had viral co-infection. The most common co-infection was by Influenza A (34.2%), Rhinovirus/Enterovirus (31.6%), other Coronaviruses (13.2). Seventeen (58.6%) patients developed super-infection. Streptococcus pneumoniae was the most frequently isolated super-infection pathogen (17.2%). Mortality occurred in 41.40% of patients with co-infection which was higher compared to the group without co-infection (32.2%) but with no statistical significance, p: 0.463. In the co-infection cohort, the deceased patients' hemoglobin (Hb), platelets count, C-reactive protein (CRP), and procalcitonin (PCT) levels were significantly different compared to survived ; 9.14 ± 1.23, 185.15± 91.42, 169.31 ± 94.91, and 2.91± 2.42 vs 10.65± 2.15 mg/dl, 249.0± 100.69 x103/μL, 59.57 ± 49.88 mg/l, and 0.55 ± 0.44 ng/ml, p value 0.044, 0.006, <0.001, and 0.012, respectively. Additionally, the deceased patient had a considerably longer ICU stay (25.75 ± 23.6 vs. 11.80 ± 11.19 days, p: 0.066). Conclusion: In SARS-CoV-2 patients, co-infection with other respiratory viruses is linked to increased mortality. The Hb and platelet counts of the deceased patients are higher than those of the survivors, while their PCT and CRP levels are lower.