Demographics and clinical characteristics of hospitalised patients under investigation for COVID-19 with an initial negative SARS-CoV-2 PCR test result

Background: The COVID-19 pandemic is placing abnormally high and ongoing demands on healthcare systems. Little is known about the full effect of the COVID-19 pandemic on diseases other than COVID-19 in the South African setting. Objective: To describe a cohort of hospitalised patients under investigation for SARS-CoV-2 that initially tested negative. Methods: Consecutive patients hospitalised at Khayelitsha Hospital from April to June 2020, whose initial polymerase chain reaction test for SARS-CoV-2 was negative were included. Patient demographics, clinical characteristics, ICD-10 (International Statistical Classification of Diseases and Related Health Problems 10th Revision) diagnosis, referral to tertiary level facilities and ICU, and all-cause in-hospital mortality were collected. The 90-day re-test rate was determined and comparisons were made using the x2-test and the independent samples median test. Results: Overall, 261 patients were included: median age 39.8 years, 55.6% female (n = 145). Frequent comorbidities included HIV (41.4%), hypertension (26.4%), and previous or current tuberculosis (24.1%). Nine (3.7%) patients were admitted to ICU and 38 (15.6%) patients died. Ninety-three patients (35.6%) were re-tested and 21 (22.6%) were positive for SARS-CoV-2. The top primary diagnoses related to respiratory diseases (n = 82, 33.6%), and infectious and parasitic diseases (n = 62, 25.4%). Thirty-five (14.3%) had a COVID-19 diagnostic code assigned (26 without microbiological confirmation) and 43 (16.5%) had tuberculosis. Older age (p = 0.001), chronic renal impairment (p = 0.03) and referral to higher level of care (all p < 0.001; ICU p = 0.03) were more frequent in those that died. Conclusion: Patients with tuberculosis and other diseases are still presenting to emergency centres with symptoms that may be attributable to SARS-CoV-2 and requiring admission. Extreme vigilance will be necessary to diagnosis and treat tuberculosis and other diseases as we emerge from the COVID-19 pandemic.