Re-infection with different SARS-CoV-2 clade and prolonged v
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The COVID 19 pandemic continues to spread worldwide. Understanding SARS-CoV-2 shedding, transmission dynamics and re-infection with different SARS-CoV-2 clades in immunocompromised persons are important clinical and public health challenges.

First admission to hospital: A 51-year-old female patient presented with a 3-day history of fever, cough, malaise and headache. Several of her family members had recently been ill with SARS-CoV-2 infection. PCR on her nasopharyngeal swab was positive for SARS-CoV-2 (Ct value of 3) and a clinical diagnosis of COVID-19 made. Five years prior to this admission, the patient had been diagnosed with follicular non-Hodgkin's lymphoma and received an autologous hematopoietic stem cell transplantation (ASCT) for which she received multiple courses of chemotherapy. She had a relapse of lymphoma and remission was achieved on Rituximab therapy.

She was also receiving monthly intravenous immunoglobulins (IVIG) for lymphoma associated hypogammaglobulinemia. She was admitted to hospital and received 7 days course of intravenous ceftriaxone for pneumonia. She improved clinically and was discharged home on day-7 post admission. The patient did not receive Remdesivir since it was not available in our hospital during this period. She did not receive steroids during this admission.

Second hospital admission: On day-19 post first admission, she was re-admitted to hospital with fever, cough and dyspnea. Her oxygen saturation was 96% at room air and the Chest X ray showed bilateral lung infiltrates. A nasopharyngeal swab PCR was positive for SARS-CoV-2, Ct value 13. Chest CT scan showed diffuse bilateral ground glass opacities. She received steroids, meropenem, and intravenous immunoglobulin (IVIG).

She received methylprednisolone 1mg/kg daily for 3 days followed by 0.5mg/kg daily for days two weeks after her admission. SARS-CoV-2 serology was negative by both ELISA and microneutralization antibody test (MNT) on day-40. She was discharged after three weeks of hospitalization and managed in the outpatient setting for presumed cryptogenic organizing pneumonia. She received 40 mg of prednisolone daily for 10 days followed by tapering doses of prednisolone over one month. Then she received 30 mg of prednisolone daily for three weeks followed by tapering doses of prednisolone over another month.. Her fever improved but she had persistent exertional dyspnea. The patient re-presented with fever and feeling unwell to the ER on day-114. A nasopharyngeal swab PCR was positive for SARS-CoV-2, (Ct=17). She was prescribed a 7-day course of ciprofloxacin for pneumonia and sent home.

Third Hospital admission: The patient was readmitted on day-160 with a history of progressive fever and dyspnea over several weeks since her last visit to ER. Her nasopharyngeal swab PCR was positive for SARS-CoV-2 (Ct value 34). Plaque assay for the tested samples showed high viral load of both the nasopharyngeal (NP) on day-31 and broncho-alveolar lavage (BAL) on day-168 compared to the positive control even at the highest dilution (106). Chest CT scan showed new ground glass opacities with air bronchogram in the right and left lower lobes. She received intravenous antibiotics (meropenem and linezolid) and dexamethasone. Bronchoscopy was performed and bronchoalveolar lavage (BAL) cytology showed reactive bronchial epithelial, alveolar macrophages and mixed inflammatory cells with no cytopathic effect noted.

Bacterial, fungal and mycobacterial cultures, and special stains for fungi and acid-fast bacilli were negative. Her serum CMV PCR was negative. Lymphocyte analysis were performed twice 6 weeks and 5 months post infection and showed CD19 B lymphocytes less than 1. Her CD4 was 540 (normal range 564-1721), her CD8 was 1670 (normal range 322-1161). Her serum IgG levels were normal during all her admissions. Five months into the third admission, repeat SARS-CoV-2 serology was still negative (ELISA and MNT) on day-165. Convalescent plasma (200 ml, SARS-CoV-2 neutralization titer 1:160) was administered as a therapeutic option, after which her COVID-19 related pneumonia resolved, and was discharged home.

She was evaluated in the infectious disease outpatient clinic on day-188. She has no fever or respiratory symptoms and SARS-CoV-2 PCR on nasopharyngeal swab was negative. The SARS-CoV-2 serology remained negative on day-213.