The temporal positivity rate of SARS-CoV-2 in different clinical samples

The temporal positivity rate of SARS-CoV-2 in different clinical samples | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Short Report The temporal positivity rate of SARS-CoV-2 in different clinical samples Fekadu Alemu, Andargachew Mulu, Eyerusalem Solomon Kebede, Dawit Hailu Alemayehu, and 12 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-2121065/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract The aim of this study is to evaluate the diagnostic value of different clinical samples from humans such as blood/serum, stool, and urine as compared to the routinely used nasopharyngeal swab samples for the detection of SARS-CoV2 in COVID-19 patients. We followed COVID-19 patients for three weeks and collected samples on three occasions that is, on the day of admission to the hospital (Day zero), after one week (Day-8), and after the second week (Day-15). The data shows that on the day of the admission of the patients, NPS has a 64% positivity rate, followed by stool, urine, and serum, 38%, 18%, and 17%, respectively. And we observed a nearly similar pattern of positivity rate in the subsequent week’s samples. SARS-CoV2 COVID-19 Stool Urine Blood Serum Nasopharyngeal swab positivity rate Figures Figure 1 Introduction Severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) which is responsible for the coronavirus disease 2019 (COVID-19) has spread all over the world since its first outbreak in early December 2019 ( 1 , 2 ). According to the COVID-19 dashboard by the Center for Systems Science and Engineering (CSSE) at John Hopkins University (JHU) ( https://coronavirus.jhu.edu/map.html ), as of August 24, 2022, 597,803,846 people were infected by the SARS-CoV2 virus, and a total of 6,458,430 deaths were recorded due to COVID-19 globally. Laboratory diagnostic testing is one of the crucial measures for curbing the spread of COVID-19. However, the quality of a laboratory test result is dependent upon the type of specimen used and the choice of diagnostic methods ( 3 , 4 ). Concerning the choice of method for the diagnosis of SARS-CoV-2, the world has agreed on using the Real-time reverse transcriptase–PCR (RT-PCR) as the standard method. Nevertheless, no consensus practical guideline recommending the appropriate type of specimen to be collected for the SARS-CoV-2 diagnosis is available ( 5 ). In our previous study which compared the positivity rate of the nasopharyngeal swab (NPS) and Saliva using 140 pairs of saliva-NPS samples, 92.14% (129/140) saliva samples tested positive for SARSA-CoV2 RNA whereas 57.14% (80/140) of NPS samples were positive, based on the finding we recommended saliva as a better alternative sample to NPS to diagnose COVID‑19 patients ( 6 ). Here, as a continuation of our previous work ( 6 ), in this report, we present data on the positivity rate of SARS-CoV2 in blood/serum, stool, and urine samples with the commonly used NPS sample. Methods Clinical samples collection and preparation All the samples were collected from symptomatic confirmed COVID-19 patients as described before in ( 6 ). The patients were admitted to St. Paul hospital five to seven days after they were confirmed positive by RT-PCR. NPS samples were collected using a viral transport medium (VTM). The first NPS, stool, blood, and urine samples were collected on the day of the patient’s admission to the hospital (hereafter, day zero), followed by the collection of two (NPS, stool, blood, and urine) samples within a one-week interval (on the 8th and 15th days). All the samples were transported from St. Paul hospital under an adequate cold chain of 4–8°C, kept refrigerated at 4°C at Armauer Hansen Research Institute, and were processed within 8–12 hours for RNA extraction. Blood samples were collected in serum separator tubes and centrifuged at 1500 rpm for 10 minutes at room temperature. Separated serum samples were aliquoted into cryotubes and stored at -80 0 C for viral nucleic acid extraction. Urine samples were collected in leak-proof screw-capped tubes and transported at 4°C. Then the urine (20–40 ml) samples were centrifuged at 2500 x g for 15 minutes at 4°C. The pellets were resuspended in 2 ml phosphate-buffered saline (PBS) and stored at -80 0 C for viral nucleic acid extraction. Stool samples were collected in a special cup (a wide-necked leak-proof screw-capped cup). Approximately 1 gram of stool was resuspended within 5 mL of normal saline, centrifuged at 10,000 rpm for 5 minutes, and 1 ml of the clarified supernatant was kept for viral detection. RNA extraction and detection Both viral RNA extraction and RNA detection by RT‑PCR were processed exactly as it has been reported previously ( 6 ). Briefly, a volume of 200 µL samples of NPS, Stool, Serum, and Urine was used to extract viral nucleic acid (NA) using DAAN Gene Co., Ltd (Da An Gene Co., Ltd, of Sun Yat-Sen University, China) extraction and purification kit. In the 200 µL of samples, 50 µL proteinase K, and 200 µL lysis buffer was added, followed by heat inactivation of the lysed samples on a dry heat block at 72°C for 10 min, the addition of inhibitor remover, and subsequent washing. The NA was eluted in 50 µL molecular grade water. Finally, the SARS-CoV2 RNA was detected using the BGI Biotechnology (Wuhan) Co.Ltd, China detection kit ( 7 ). Results On the day of the admission of the patients (on Day-zero or within five to seven days after the patients were confirmed positive by RT-PCR), NPS has a 64% positivity rate, followed by stool, urine, and serum, 38%, 18%, and 17%, respectively. A similar pattern of positivity rate has been observed in the samples collected on the second and third week of the follow-up that is, NPS has the highest positivity rate followed by stool, urine, and serum (Table 1 ). Detailed data with the Ct values are presented in the Additional file1. Table 1 SARS-CoV2 positivity rate over time (Day-0, Day-8, and Day-15) where ‘N’ represents the total number of patient samples, positives, and negatives processed. Nasopharyngeal swab Day-0 (N) Day-0 Positivity rate Day-8 (N) Day-8 Positivity rate Day-15 (N) Day-15 Positivity rate Total sample 152 70 14 Positive 98 64.47 23 32.86 8 57.14 Negative 54 35.53 47 67.14 6 42.86 Serum Total sample 136 67 14 Positive 23 16.91 8 11.94 1 7.14 Negative 113 83.09 59 88.06 13 92.86 Stool Total sample 45 28 5 Positive 17 37.78 7 25 1 20 Negative 28 62.22 21 75 4 80 Urine Total sample 76 36 7 Positive 14 18.42 4 11.11 1 14.29 Negative 62 81.58 32 88.89 6 85.71 Considering that sample collection began almost a week after the patients confirmed positive and were admitted to the hospital, we followed them for three consecutive weeks; this shows that there is shedding of the virus up to the fourth week. In addition, a clear pattern of viral load decrease over time has been observed particularly for NPS, serum, and Stool samples (Fig. 1 ). Discussion Our study shows that SARS-CoV2 RNA was detected in all types of clinical samples tested, including NPS, serum, stool, and urine. The highest positivity rate was detected in NPS followed by stool while the lowest was from the serum sample. Similarly, the lowest Ct value (meaning high viral load) was detected in the NPS and stool samples. This implies that NPS is the most appropriate clinical specimen( 8 ), and stool is the most preferred specimen next to NPS. However, our data is in contrast to this study ( 8 ), which reported no detection of SARS-CoV-2 in urine and serum. Even though we reported a high positivity rate in NPS, there were few observations where samples from NPS detected no SARS-CoV2 while other specimens turn out to be positive for the virus. This shows the need for testing specimens from multiple sites to improve the sensitivity and reduce false-negative test results ( 4 ). Because saliva is more sensitive than NPS and easy to collect for COVID-19 diagnosis ( 6 , 9 ), the use of a combination of saliva, NPS, and stool sample greatly improves the sensitivity and reduces false negative test results of COVID-19 diagnosis. Declarations Ethics approval and consent to participate: The study is approved by the Armauer Hansen Research Institute/ALERT Ethics Review Committee. And informed consent was obtained from all study participants. All methods were performed in accordance with the guidelines and regulations stipulated in the Ethiopian national comprehensive COVID-19 management handbook. Consent for publication: Not applicable. Availability of data and materials : All data generated or analyzed during this study are available (Additional file1). Competing interests: The authors declare no competing interests. Funding: The author(s) received no specific funding for this work. Author contributions Conceived the project idea: AM, GTB, AA, AdM, and LY. Conducted laboratory work: FA, ESK, DHA, TS, DAT, GA, AT, AH, GB, BT, and MY. Data analysis: FA, GTB, AA, AdM, and LY. Wrote – the original draft: GTB, FA, AM, AA, and AdM. Writing – review & editing: GTB, FA, AM, GTB, AA, AdM, and LY. References Cucinotta D, Vanelli M. WHO declares COVID-19 a pandemic. Acta Biomed. 2020;91(1):157–60. Di Nardo M, van Leeuwen G, Loreti A, Barbieri MA, Guner Y, Locatelli F, et al. A literature review of 2019 novel coronavirus (SARS-CoV2) infection in neonates and children. Pediatr Res [Internet]. 2020;(April):1–8. Available from: http://dx.doi.org/10.1038/s41390-020-1065-5 . Zhurakivska K, Troiano G, Pannone G, Caponio VCA, Lo Muzio L. An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens. Front Public Heal. 2020;8(August):1–9. Bwire GM, Majigo MV, Njiro BJ, Mawazo A. Detection profile of SARS-CoV-2 using RT-PCR in different types of clinical specimens: A systematic review and meta-analysis. J Med Virol. 2021;93(2):719–25. Luvira V, Jittmittraphap A, Muangnoicharoen S, Chantawat N, Janwitthayanan W, Leaungwutiwong P. Temporal change of SARS-CoV-2 in clinical specimens of COVID-19 pneumonia patients. Am J Trop Med Hyg. 2020;103(3):1204–6. Beyene GT, Alemu F, Kebede ES, Alemayehu DH, Seyoum T, Tefera DA, et al. Saliva is superior over nasopharyngeal swab for detecting SARS - CoV2 in COVID – 19 patients. Sci Rep [Internet]. 2021;1–6. Available from: https://doi.org/10.1038/s41598-021-02097-2 . BGI Genomics Co. Ltd. Real-Time Fluorescent RT-PCR Kit for Detecting SARS-2019-CoV2. 2020. Sharma K, Aggarwala P, Gandhi D, Mathias A, Singh P, Sharma S, et al. Comparative analysis of various clinical specimens in detection of SARS-CoV-2 using rRT-PCR in new and follow up cases of COVID-19 infection: Quest for the best choice. PLoS One [Internet]. 2021;16(4 April). Available from: http://dx.doi.org/10.1371/journal.pone.0249408 . Teo AKJ, Choudhury Y, Tan IB, Cher CY, Chew SH, Wan ZY, et al. Saliva is more sensitive than nasopharyngeal or nasal swabs for diagnosis of asymptomatic and mild COVID-19 infection. Sci Rep [Internet]. 2021;11(1):1–8. Available from: https://doi.org/10.1038/s41598-021-82787-z . Additional Declarations No competing interests reported. Supplementary Files Additionalfile1.xlsx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. 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Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-2121065","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Short Report","associatedPublications":[],"authors":[{"id":141696001,"identity":"9833bd1b-5772-4a11-bc6c-19d0728e9793","order_by":0,"name":"Fekadu Alemu","email":"","orcid":"","institution":"Armauer Hansen Research institute, Jumma Road ALERT Compound","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Fekadu","middleName":"","lastName":"Alemu","suffix":""},{"id":141696002,"identity":"962e14d1-2ae1-4777-8bf8-a4a4a3971d02","order_by":1,"name":"Andargachew Mulu","email":"","orcid":"","institution":"Armauer 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15:29:27","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-2121065/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-2121065/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":27395448,"identity":"f18dbc32-eb71-4e24-b87e-02e0183e77ad","added_by":"auto","created_at":"2022-10-05 20:52:34","extension":"jpg","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":237700,"visible":true,"origin":"","legend":"\u003cp\u003eTemporal shedding of SARS-CoV2 in NPS, Serum, Stool, and Urine samples as expressed by the Ct values. The nested scatter plots of each clinical sample from left to right represent positive data points from Day-0, Day-8, and day-15. All the positive data points can be obtained from Table 1.\u003c/p\u003e","description":"","filename":"1.jpg","url":"https://assets-eu.researchsquare.com/files/rs-2121065/v1/c8a845a5183f524e59439f61.jpg"},{"id":27729927,"identity":"84eb3adb-e927-4ab8-a2f6-f65cbd2fd92d","added_by":"auto","created_at":"2022-10-13 14:29:18","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":356154,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-2121065/v1/c4586658-89ae-4742-9558-83dd4782a80e.pdf"},{"id":27395447,"identity":"ca888047-6ba1-4335-be92-8e38b9b9a9d1","added_by":"auto","created_at":"2022-10-05 20:52:34","extension":"xlsx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":21725,"visible":true,"origin":"","legend":"","description":"","filename":"Additionalfile1.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-2121065/v1/a5f6bdfeb85113028ee964ec.xlsx"}],"financialInterests":"No competing interests reported.","formattedTitle":"The temporal positivity rate of SARS-CoV-2 in different clinical samples","fulltext":[{"header":"Introduction","content":"\u003cp\u003eSevere acute respiratory syndrome coronavirus 2 (SARS-CoV2) which is responsible for the coronavirus disease 2019 (COVID-19) has spread all over the world since its first outbreak in early December 2019 (\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e). According to the COVID-19 dashboard by the Center for Systems Science and Engineering (CSSE) at John Hopkins University (JHU) (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://coronavirus.jhu.edu/map.html\u003c/span\u003e\u003cspan address=\"https://coronavirus.jhu.edu/map.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e), as of August 24, 2022, 597,803,846 people were infected by the SARS-CoV2 virus, and a total of 6,458,430 deaths were recorded due to COVID-19 globally.\u003c/p\u003e \u003cp\u003eLaboratory diagnostic testing is one of the crucial measures for curbing the spread of COVID-19. However, the quality of a laboratory test result is dependent upon the type of specimen used and the choice of diagnostic methods (\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e). Concerning the choice of method for the diagnosis of SARS-CoV-2, the world has agreed on using the Real-time reverse transcriptase\u0026ndash;PCR (RT-PCR) as the standard method. Nevertheless, no consensus practical guideline recommending the appropriate type of specimen to be collected for the SARS-CoV-2 diagnosis is available (\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e). In our previous study which compared the positivity rate of the nasopharyngeal swab (NPS) and Saliva using 140 pairs of saliva-NPS samples, 92.14% (129/140) saliva samples tested positive for SARSA-CoV2 RNA whereas 57.14% (80/140) of NPS samples were positive, based on the finding we recommended saliva as a better alternative sample to NPS to diagnose COVID‑19 patients (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e). Here, as a continuation of our previous work (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e), in this report, we present data on the positivity rate of SARS-CoV2 in blood/serum, stool, and urine samples with the commonly used NPS sample.\u003c/p\u003e"},{"header":"Methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eClinical samples collection and preparation\u003c/h2\u003e \u003cp\u003eAll the samples were collected from symptomatic confirmed COVID-19 patients as described before in (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e). The patients were admitted to St. Paul hospital five to seven days after they were confirmed positive by RT-PCR. NPS samples were collected using a viral transport medium (VTM). The first NPS, stool, blood, and urine samples were collected on the day of the patient\u0026rsquo;s admission to the hospital (hereafter, day zero), followed by the collection of two (NPS, stool, blood, and urine) samples within a one-week interval (on the 8th and 15th days). All the samples were transported from St. Paul hospital under an adequate cold chain of 4\u0026ndash;8\u0026deg;C, kept refrigerated at 4\u0026deg;C at Armauer Hansen Research Institute, and were processed within 8\u0026ndash;12 hours for RNA extraction. Blood samples were collected in serum separator tubes and centrifuged at 1500 rpm for 10 minutes at room temperature. Separated serum samples were aliquoted into cryotubes and stored at -80\u003csup\u003e0\u003c/sup\u003eC for viral nucleic acid extraction. Urine samples were collected in leak-proof screw-capped tubes and transported at 4\u0026deg;C. Then the urine (20\u0026ndash;40 ml) samples were centrifuged at 2500 x g for 15 minutes at 4\u0026deg;C. The pellets were resuspended in 2 ml phosphate-buffered saline (PBS) and stored at -80\u003csup\u003e0\u003c/sup\u003eC for viral nucleic acid extraction. Stool samples were collected in a special cup (a wide-necked leak-proof screw-capped cup). Approximately 1 gram of stool was resuspended within 5 mL of normal saline, centrifuged at 10,000 rpm for 5 minutes, and 1 ml of the clarified supernatant was kept for viral detection.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eRNA extraction and detection\u003c/h2\u003e \u003cp\u003eBoth viral RNA extraction and RNA detection by RT‑PCR were processed exactly as it has been reported previously (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e). Briefly, a volume of 200 \u0026micro;L samples of NPS, Stool, Serum, and Urine was used to extract viral nucleic acid (NA) using DAAN Gene Co., Ltd (Da An Gene Co., Ltd, of Sun Yat-Sen University, China) extraction and purification kit. In the 200 \u0026micro;L of samples, 50 \u0026micro;L proteinase K, and 200 \u0026micro;L lysis buffer was added, followed by heat inactivation of the lysed samples on a dry heat block at 72\u0026deg;C for 10 min, the addition of inhibitor remover, and subsequent washing. The NA was eluted in 50 \u0026micro;L molecular grade water. Finally, the SARS-CoV2 RNA was detected using the BGI Biotechnology (Wuhan) Co.Ltd, China detection kit (\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e).\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cp\u003eOn the day of the admission of the patients (on Day-zero or within five to seven days after the patients were confirmed positive by RT-PCR), NPS has a 64% positivity rate, followed by stool, urine, and serum, 38%, 18%, and 17%, respectively. A similar pattern of positivity rate has been observed in the samples collected on the second and third week of the follow-up that is, NPS has the highest positivity rate followed by stool, urine, and serum (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Detailed data with the Ct values are presented in the Additional file1.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eSARS-CoV2 positivity rate over time (Day-0, Day-8, and Day-15) where \u0026lsquo;N\u0026rsquo; represents the total number of patient samples, positives, and negatives processed.\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"7\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNasopharyngeal swab\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eDay-0 (N)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eDay-0 Positivity rate\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eDay-8 (N)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eDay-8 Positivity rate\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eDay-15 (N)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eDay-15 Positivity rate\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal sample\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e152\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e70\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePositive\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e64.47\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e32.86\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e57.14\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e54\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e35.53\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e47\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e67.14\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e42.86\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSerum\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"6\" nameend=\"c7\" namest=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal sample\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e136\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e67\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePositive\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e23\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e16.91\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e11.94\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e7.14\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e113\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e83.09\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e59\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e88.06\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e13\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e92.86\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eStool\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"6\" nameend=\"c7\" namest=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal sample\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e45\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePositive\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e17\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e37.78\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e25\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e20\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e28\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e62.22\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e21\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e75\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e80\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUrine\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colspan=\"6\" nameend=\"c7\" namest=\"c2\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTotal sample\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e76\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e36\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e\u0026nbsp;\u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003ePositive\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e14\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e18.42\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e11.11\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e14.29\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNegative\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c2\"\u003e \u003cp\u003e62\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003e\u003cb\u003e81.58\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003e32\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c5\"\u003e \u003cp\u003e\u003cb\u003e88.89\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c6\"\u003e \u003cp\u003e6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e\u003cb\u003e85.71\u003c/b\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003eConsidering that sample collection began almost a week after the patients confirmed positive and were admitted to the hospital, we followed them for three consecutive weeks; this shows that there is shedding of the virus up to the fourth week. In addition, a clear pattern of viral load decrease over time has been observed particularly for NPS, serum, and Stool samples (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eOur study shows that SARS-CoV2 RNA was detected in all types of clinical samples tested, including NPS, serum, stool, and urine. The highest positivity rate was detected in NPS followed by stool while the lowest was from the serum sample. Similarly, the lowest Ct value (meaning high viral load) was detected in the NPS and stool samples. This implies that NPS is the most appropriate clinical specimen(\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e), and stool is the most preferred specimen next to NPS. However, our data is in contrast to this study (\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e), which reported no detection of SARS-CoV-2 in urine and serum. Even though we reported a high positivity rate in NPS, there were few observations where samples from NPS detected no SARS-CoV2 while other specimens turn out to be positive for the virus. This shows the need for testing specimens from multiple sites to improve the sensitivity and reduce false-negative test results (\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e). Because saliva is more sensitive than NPS and easy to collect for COVID-19 diagnosis (\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e), the use of a combination of saliva, NPS, and stool sample greatly improves the sensitivity and reduces false negative test results of COVID-19 diagnosis.\u003c/p\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate:\u0026nbsp;\u003c/strong\u003eThe study is approved by the Armauer Hansen Research Institute/ALERT Ethics Review Committee. And informed consent was obtained from all study participants. All methods were performed in accordance with the guidelines and regulations stipulated in the Ethiopian national comprehensive COVID-19 management handbook.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication:\u0026nbsp;\u003c/strong\u003eNot applicable.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e: All data generated or analyzed during this study are available (Additional file1).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests:\u0026nbsp;\u003c/strong\u003eThe authors declare no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding:\u0026nbsp;\u003c/strong\u003eThe author(s) received no specific funding for this work.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003e\u0026nbsp;Author contributions\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eConceived the project idea: AM, GTB, AA, AdM, and LY. Conducted laboratory work: FA, ESK, DHA, TS, DAT, GA, AT, AH, GB, BT, and MY. Data analysis: FA, GTB, AA, AdM, and LY. Wrote \u0026ndash; the original draft: GTB, FA, AM, AA, and AdM. Writing \u0026ndash; review \u0026amp; editing: GTB, FA, AM, GTB, AA, AdM, and LY.\u0026nbsp;\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eCucinotta D, Vanelli M. WHO declares COVID-19 a pandemic. Acta Biomed. 2020;91(1):157\u0026ndash;60.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDi Nardo M, van Leeuwen G, Loreti A, Barbieri MA, Guner Y, Locatelli F, et al. A literature review of 2019 novel coronavirus (SARS-CoV2) infection in neonates and children. Pediatr Res [Internet]. 2020;(April):1\u0026ndash;8. Available from: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://dx.doi.org/10.1038/s41390-020-1065-5\u003c/span\u003e\u003cspan address=\"10.1038/s41390-020-1065-5\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eZhurakivska K, Troiano G, Pannone G, Caponio VCA, Lo Muzio L. An Overview of the Temporal Shedding of SARS-CoV-2 RNA in Clinical Specimens. Front Public Heal. 2020;8(August):1\u0026ndash;9.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBwire GM, Majigo MV, Njiro BJ, Mawazo A. Detection profile of SARS-CoV-2 using RT-PCR in different types of clinical specimens: A systematic review and meta-analysis. J Med Virol. 2021;93(2):719\u0026ndash;25.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLuvira V, Jittmittraphap A, Muangnoicharoen S, Chantawat N, Janwitthayanan W, Leaungwutiwong P. 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Available from: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41598-021-82787-z\u003c/span\u003e\u003cspan address=\"10.1038/s41598-021-82787-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"SARS-CoV2, COVID-19, Stool, Urine, Blood, Serum, Nasopharyngeal swab, positivity rate","lastPublishedDoi":"10.21203/rs.3.rs-2121065/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-2121065/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eThe aim of this study is to evaluate the diagnostic value of different clinical samples from humans such as blood/serum, stool, and urine as compared to the routinely used nasopharyngeal swab samples for the detection of SARS-CoV2 in COVID-19 patients. We followed COVID-19 patients for three weeks and collected samples on three occasions that is, on the day of admission to the hospital (Day zero), after one week (Day-8), and after the second week (Day-15). The data shows that on the day of the admission of the patients, NPS has a 64% positivity rate, followed by stool, urine, and serum, 38%, 18%, and 17%, respectively. And we observed a nearly similar pattern of positivity rate in the subsequent week\u0026rsquo;s samples.\u003c/p\u003e","manuscriptTitle":"The temporal positivity rate of SARS-CoV-2 in different clinical samples","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2022-10-05 20:52:32","doi":"10.21203/rs.3.rs-2121065/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"77b31502-0635-4e0e-824f-e3623a931b70","owner":[],"postedDate":"October 5th, 2022","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2022-10-13T14:29:14+00:00","versionOfRecord":[],"versionCreatedAt":"2022-10-05 20:52:32","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-2121065","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-2121065","identity":"rs-2121065","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}