Here we present a description of severe COVID-19 infection with extrapulmonary manifestation in infant at a time when the prevalent SARS-CoV-2 strain was the so-called Omicron variant. A male infant, born at 38 weeks' gestation, was admitted to the emergency department on January 31, 2022 due to congenital pneumonia. A chest X-ray showed interstitial pneumonia, however, RT PCR of the patient’s nasopharyngeal swab sample was negative for SARS-CoV-2, as well as for other respiratory viruses. The most common causes of congenital pneumonia, including TORCH-infections, chlamydia, and other pathogens that colonize the mother’s birth canal, were ruled out. On admission, the infant had respiratory failure (SpO₂-88%) and required 7 days of high-flow oxygen. Empirical antimicrobial treatment (ceftriaxone 80 mg/kg every 24h, amikacin 7,5 mg/kg every 12h) was initiated intravenously. Over the following week, there was gradual improvement in respiratory function. The infant was discharged from the hospital.

Three month later, the infant presented to the infectious disease department following a 3-day history of fever, coughing, poor feeding and limitation of movement in the right hip and knee joints. RT-PCR analysis of the nasopharyngeal swab sample of the infant and his mother was positive for SARS-CoV-2. On initial assessment, the infant was in febril convulsions with marble skin, acrocyanosis. Auscultation of the lungs revealed decreased breathing. His total leukocyte count was high 26,41x 10⁹/L, absolute lymphocyte count was 8,17x10⁹/L, absolute neutrophil count was 15,09x10⁹/L, SpO₂-90%. The levels of blood inflammatory markers, including ferritin, C-reactive protein, and procalcitonin were 507ng/ml, 195mg/L and 2,10ng/ml respectively. A blood serological test for HIV was also performed, and it was negative. Bacterial cultures of blood, urine and respiratory secretions were negative. Chest radiography showed bilateral airspace opacification. Ultrasound examination revealed thickening of the synovial bursa and edema of the right hip and knee joints.

After antimicrobial (intravenous ceftazidime) and antiviral (remdesivir for 5 days) treatment, the patient’s respiratory and joint functions gradually improved. Notably, over the following 3 weeks, the infant’s nasopharyngeal swab sample was positive for SARS-CoV-2, suggesting that the infant was immunocompromised. After a negative result for SARS-CoV-2 on hospital day 30, the patient was transferred to another hospital to determine the cause of the possible immunodeficiency.