SARS-CoV-2 RNA Detection in Gastrointestinal Sample Displays Poor Performance

Abstract

We have recently read with interest the recent article titled “Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples from the Hong Kong Cohort and Systematic Review and Meta-analysis”1Cheung K.S. et al.Gastroenterology. 2020; 159: 81-95Abstract Full Text Full Text PDF PubMed Scopus (958) Google Scholar published in Gastroenterology. The authors concluded that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA could be detected in stool samples from 48.1% of patients. However, the pragmatic usefulness of SARS-CoV-2 RNA detection in gastrointestinal sample needs to be evaluated. Real-time reverse transcriptase-polymerase chain reaction (rRT-PCR) typically has been used for SARS-CoV-2 detection. To compare the SARS-CoV-2 rRT-PCR of gastrointestinal sample versus respiratory sample for diagnostic performance of the coronavirus disease 2019 (COVID-19), we performed a retrospective analysis of patients from the East Branch of the Renmin Hospital of Wuhan University (a designated hospital for critical care), China between January and March, 2020. All patients treated by the medical assistance teams from hospitals all over the country and diagnosed as having COVID-19 according to World Health Organization interim guidance, were recruited if they were tested for SARS-CoV-2 RNA of gastrointestinal samples during their hospital stay. The rRT-PCR assay simultaneously amplified and tested two reported target genes of SARS-CoV-2, including open reading frame 1ab (ORF1ab) and nucleocapsid protein (N).2Wang D. et al.JAMA. 2020; 323: 1843-1844PubMed Google Scholar The state of SARS-CoV-2 RNA at the detection time was determined by all rRT-PCR results of all samples (including nasopharyngeal swabs, feces, sputum, anal swabs, bronchoalveolar lavage fluid, and urine) in a specific period: if any one was positive, it was defined SARS-CoV-2 RNA (+), otherwise SASR-CoV-2 RNA (-). The specific period was from the day before the detection to hospital discharge. An Informed Consent for Exempt and Minimal Risk Research was approved by the ethics committee of West China Hospital and reported to the National Health Commission. All rRT-PCR results were collected from 144 confirmed patients (67 male, 77 female; age, 20–87 years), including 853 results of nasopharyngeal swabs, 232 results of sputum samples, 195 results of gastrointestinal samples, and 34 results of other samples (like urine and bronchoalveolar lavage fluid samples). As shown in Supplementary Table 1, the positive detection rates of nasopharyngeal swabs (312/550, 56.7%; 95% confidence interval [CI], 52.6%–60.9%) and sputum samples (74/148, 50.0%; 95% CI, 41.9%–58.1%) were significantly higher than those of fecal samples (17/99, 17.2%; 95% CI, 9.6%–24.7%) and anal swabs (22.6%; 95% CI, 11.0%–34.3%) in the indirect comparisons (all P < .05). Each result of fecal sample or anal swab was matched with the corresponding result of nasopharyngeal swab or sputum sample nearest to its time. The simultaneous examinations with various samples were performed for directly comparing the diagnostic value. The positive detection rate of nasopharyngeal swab test was similar to that of sputum sample test (P = .705), but was significantly higher than that of anal swab and fecal sample test (all P < .001; Supplementary Table 1). Moreover, SARS-CoV-2 (+) was associated with the increased IgM antibody (P = .004) and decreased IgG antibodies (P < .001) in COVID-19 patients (all P < .05). However, no significant difference was observed in the subgroup analysis of specimen type (all P > .05). COVID-19 has a high incidence and rapid infection, and has become a huge threat to global public health. Previous studies have shown that SARS-CoV-2 can infect gastrointestinal cells and remain in feces,3Xiao F. et al.Gastroenterology. 2020; 158: 1831-1833Abstract Full Text Full Text PDF PubMed Scopus (1748) Google Scholar,4Du M.L. et al.Gastroenterology. 2020; 158: 2298-2301Abstract Full Text Full Text PDF PubMed Scopus (82) Google Scholar which creates the potential for fecal–oral viral transmission.5Chan J.F. et al.Lancet. 2020; 395: 514-523Abstract Full Text Full Text PDF PubMed Scopus (5559) Google Scholar,6Gu J.Y. et al.Gastroenterology. 2020; 158: 1518-1519Abstract Full Text Full Text PDF PubMed Scopus (929) Google Scholar Also, gastrointestinal symptoms like diarrhea have been frequently reported.7Cholankeril G. et al.Gastroenterology. 2020; 159: 775-777Abstract Full Text Full Text PDF PubMed Scopus (134) Google Scholar,8D’Amico F. et al.Clin Gastroenterol Hepatol. 2020; 18: 1663-1672Abstract Full Text Full Text PDF PubMed Scopus (333) Google Scholar Our data suggested that rRT-PCR test of gastrointestinal sample had limited value for diagnosis of COVID-19. Finding This illustrated that, as a method to screen and monitor whether the virus exists, gastrointestinal sample testing for SARS-CoV-2 RNA displays poor performance. Although both of them had low positive detection rates, the efficiency of rRT-PCR test of respiratory sample was better than that of gastrointestinal sample. In terms of health economics, nasopharyngeal swab and sputum sample tests are more cost effective than gastrointestinal sample test and should be a main sampling method for diagnosing SARS-CoV-2 infection in the epidemic areas with limited resources. Furthermore, the state of SARS-CoV-2 RNA might depend on the level of IgM/IgG antibody, rather than on the specimen type. Some indistinct trends of association between IgM/IgG antibody level and result of fecal sample test for SARS-CoV-2 RNA were observed (P = .096 and P = .044), probably because of the low positive detection rate. The patient's benefit for diagnosis from conducting a gastrointestinal sample test for SARS-CoV-2 RNA was far from enough, compared with that of a nasopharyngeal swab or sputum sample test. Supplementary Table 1Positive Detection Rates of SARS-CoV-2 rRT-PCR Results of Gastrointestinal Samples and Respiratory SamplesrRT-PCR +SARS-CoV-2 RNA +Positive detection rate (95% CI)P valueNasopharyngeal swab Nucleocapsid protein25855046.9% (42.7% to 51.1%) Open reading frame 1ab23455042.5% (38.4% to 46.7%) Combination31255056.7% (52.6% to 60.9%)Sputum sample Nucleocapsid protein5814839.2% (31.2% to 47.1%) Open reading frame 1ab5314835.8% (28.0% to 43.6%) Combination7414850.0% (41.9% to 58.1%)Fecal sample Nucleocapsid protein139913.1% (6.4% to 19.9%) Open reading frame 1ab149914.1% (7.2% to 21.1%) Combination179917.2% (9.6% to 24.7%)Anal swab Nucleocapsid protein95317.0% (6.5% to 27.4%) Open reading frame 1ab3535.7% (–0.8% to 12.1%) Combination125322.6% (11.0% to 34.3%)Nasopharyngeal swab vs sputum sampleaEach pair of 2 tests was matched according to the closest time. Nasopharyngeal swab5612744.1% (35.3% to 52.8%).705 Sputum sample5912746.5% (37.7% to 55.2%)Nasopharyngeal swab vs. fecal sampleaEach pair of 2 tests was matched according to the closest time. Nasopharyngeal swab479151.6% (41.2% to 62.1%)<.001 Fecal sample159116.5% (8.7% to 24.3%)Nasopharyngeal swab vs. anal swabaEach pair of 2 tests was matched according to the closest time. Nasopharyngeal swab284957.1% (42.8% to 71.5%)<.001 Anal swab114922.4% (10.3% to 34.6%)Sputum sample vs. fecal sampleaEach pair of 2 tests was matched according to the closest time. Sputum sample214645.7% (30.7% to 60.6%)<.001 Fecal sample54610.9% (1.5% to 20.2%)Sputum sample vs. anal swabaEach pair of 2 tests was matched according to the closest time. Sputum sample71258.3% (25.6% to 91.1%).219 Anal swab41233.3% (2.0% to 64.6%)Fecal sample vs. anal swabaEach pair of 2 tests was matched according to the closest time. Fecal sample08–.068 Anal swab4850.0% (5.3% to 94.7%)CI, confidence interval; RNA, ribose nucleic acid; rRT-PCR, real-time reverse transcription-polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.a Each pair of 2 tests was matched according to the closest time. Open table in a new tab CI, confidence interval; RNA, ribose nucleic acid; rRT-PCR, real-time reverse transcription-polymerase chain reaction; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2. Gastrointestinal Manifestations of SARS-CoV-2 Infection and Virus Load in Fecal Samples From a Hong Kong Cohort: Systematic Review and Meta-analysisGastroenterologyVol. 159Issue 1PreviewInfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), which has been characterized by fever, respiratory, and gastrointestinal symptoms as well as shedding of virus RNA into feces. We performed a systematic review and meta-analysis of published gastrointestinal symptoms and detection of virus in stool and also summarized data from a cohort of patients with COVID-19 in Hong Kong. Full-Text PDF ReplyGastroenterologyVol. 160Issue 3PreviewWe thank Xing et al1 for their findings on the comparison of detection rates of different samples (nasopharyngeal swabs, sputum samples, gastrointestinal samples, and others like urine and bronchoalveolar lavage) for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in response to our recent study.2 In their cohort of 144 patients with coronavirus disease-2019 (COVID-19), the positive rate of nasopharyngeal swab (56.7%) was similar to that of sputum (50.0%), but was higher than stool samples (17.2%) and anal swab (22.6%). Full-Text PDF