Identification of bacterial lung infections and pre-existing persistent/chronic viral infections in COVID-19 patients

To date, there is no information about co-existing bacterial lung infections and chronic/persistent virus infections of COVID-19 patients in Latvia so the aim of this study was to identify such co-infections. In total 112 [51 (45.5%) male, median age 61 years; 60 (53.6%) female, median age 65 years; the gender of one 79 years old patient was unknown] hospitalized COVID-19 patients were included in this study. Presence of 7 respiratory bacteria (Chlamydophila pneumoniae, Mycoplasma pneumoniae, Legionella pneumophila, Bordetella pertussis, Bordetella parapertussis, Streptococcus pneumoniae and Haemophilus influenzae) was tested in 112 DNA samples isolated from oropharyngeal swabs and presence of 12 viruses (herpes simplex virus 1 and 2, varicella zoster virus, Epstein-Barr virus, cytomegalovirus, human herpes virus 6 and 7, human adenovirus, human parechovirus, human enterovirus, mumps virus and parvovirus B19) in 81 DNA samples isolated from peripheral blood mononuclear cells (PBMC) and cell-free blood plasma was tested by multiplex PCR (Allplex Respiratory Panel 4, Allplex Meningitis-V1 Assay and Allplex Meningitis-V2 Assay, Seegene Inc., Republic of Korea). In total 5 out of 112 (4.5%) oropharyngeal swabs were Haemophilus influenzae positive, while 2 out of 112 (1.8%) – were Streptococcus pneumoniae positive. 30 out of 81 (37%) PBMC samples were Epstein-Barr virus positive, 17 out of 81 (21%) samples were human herpes virus 7 positive and one sample – human herpes virus 6 positive. No plasma samples were positive for any of viruses tested. For 6 (7.4%) patients co-infection of Epstein-Barr virus and human herpes virus 7 was detected, and for one patient – Epstein-Barr virus and human herpes virus 6 was detected. Co-infections with respiratory bacteria are not common among hospitalized COVID-19 patients in Latvia. Chronic/persistent Epstein-Barr virus infection is the most common co-infection present among hospitalized COVID-19 patients in Latvia, followed by human herpes virus 7 infection.