Comparison of SARS-CoV-2 RNA detection in different types of clinical specimens among suspected COVID-19 patients in Addis Ababa, Ethiopia.

Although nasopharyngeal swabs (NPSs) are superior to saliva specimens, saliva can be used as an alternative specimen for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. Moreover, studies have reported contradicting findings on whether SARS-CoV-2 can be detected in urine or not. Thus, we aimed to evaluate the diagnostic utility of NPSs, saliva and urine specimens in suspected COVID-19 patients. We conducted a cross-sectional study among a total of 604 specimens collected from 219 individuals suspected for COVID-19 from February to July 2022. We recruited participants from two COVID-19 isolation and treatment centers in Addis Ababa. We analyzed the specimens by real-time reverse transcriptase polymerase chain reaction (RT-PCR) with a Cobas 8800 automated system. The presence of SARS-CoV-2 in NPS, saliva, and urine samples was measured by cycle threshold (Ct) values. Descriptive statistics such as frequency, percent, and mean with standard deviation were used to summarize participants characteristics. We conducted chi-square test to compare RT‒PCR results of NPS, saliva and urine specimens. All data was analyzed by SPSS version 27, and the level of significance was set at a p value ≤ 0.05. Of the 219 participants, 126 (57.5%) were positive for SARS-CoV-2 either from NPS, saliva, urine or all specimens. The rate of SARS-CoV-2 detection was significantly higher in NPS (53.9%) than in saliva (35.2%; p = 0.001) and urine (9.0%; p = 0.001) specimens. The percentage of positive agreement between NPS and saliva was 92.2%, while negative agreement was 66.9%. The overall agreement between NPS and saliva was 75.8% (K = 0.53, p < 0.001). In addition, there was a significant correlation in Ct values of both ORF1ab and E genes between the paired NPS and saliva specimens. There was significant positive correlation between NPS and saliva specimens Ct values of both ORF1ab and E genes and days from onset of symptoms to specimen collection. SARS-CoV-2 was significantly detected in NPS than in saliva and urine specimens. Although NPS is better for SARS-CoV-2 detection, saliva specimen can be used as an alternative clinical specimen in resource-limited settings where access to swabs is limited. Both saliva and urine could be sources of viral transmission.

Supplementary information: The online version contains supplementary material available at 10.1007/s13337-024-00892-9.