key: cord-0821825-xkhokdj3 authors: Zhou, J.; Chen, L.; Zhang, D.; Chen, H.; Sheng, Q.; Deng, H.; Zhang, Y.; Ni, S.; Luo, S.; Ren, B. title: Optimal upper respiratory tract sampling time for novel coronavirus pneumonia suspects date: 2020-05-09 journal: nan DOI: 10.1101/2020.05.06.20069302 sha: 7a17c6038543f83bea6dac9b53409f5beb76a70e doc_id: 821825 cord_uid: xkhokdj3 Objective: Explore best upper respiratory tract sampling time of suspected novel coronavirus pneumonia cases. Methods: We collected dates of patients from Hangzhou, Shenzhen, Jinhua city and so on who had the clear exposure history of a novel coronavirus pneumonia(COVID-19). We retrospected demographic data, exposure time, onset time, visiting time and positive time for novel coronavirus nucleic acid detection in respiratory specimens. There were 256 patients from January 20, 2020-February 12,2020 from eight cities included in our study. 106 cases appeared symptoms before January 25th and 150 after. Results: There were 136(53.1%)male infected cases. The mean age of all patients was 43.80 {+/-} 14.85.The median time from exposure to onset was 5(3,8)days.The median time of the first time of positive nucleic acid detection was 11(9,14)days and mode number was 13.The median time from onset to the first time of positive nucleic acid detection was 6(4,8)days and mode number was 5. The time from onset to definite diagnosis was 5(3,7) days before January 25th while it was 7.5(5,10)days after which was significantly shorter before January 25th(U=3885.5,P<0.001). The time from exposure to definite diagnosis was 11(9,14)days and 11(9,14)days before January 25th and after and without significant difference. The time from exposure to definite diagnosis was 11(9,13)days in first-tier cities and 13(11,15)days in second and third-tier cities. The difference was significantly shorter of first-tier cities(U=1355.5 P=0.039). And also the time was short from visiting to definite diagnosis which was 2(2,3)days in first-tier cities and 3(2,4)days in second and third-tier cities but without significant difference(U=842.5P=0.054). Conclusions: From our study we found that the best upper respiratory tract sampling time for novel coronavirus pneumonia suspects was 13days after exposure. The time from onset to definite diagnosis was shorter after January 25th. The patients were diagnosed faster in the first-tier cities after exposure. time, visiting time and positive time for novel coronavirus nucleic acid detection in respiratory specimens. There were 256 patients from January 20,2020-February 12,2020 from eight cities included in our study. 106 cases appeared symptoms before January 25 th and 150 after. Results: There were 136(53.1%)male infected cases. The mean age of all patients was 43.80±14.85.The median time from exposure to onset was 5 (3, 8) days.The median time of the first time of positive nucleic acid detection was 11 (9, 14) days and mode number was 13.The median time from onset to the first time of positive nucleic acid detection was 6 (4, 8) days and mode number was 5.The time from onset to definite diagnosis was 5 (3, 7) days before January 25 th while it was 7.5(5,10)days after which was significantly shorter before January 25 th (U=3885.5,P<0.001). The time from exposure to definite diagnosis was 11 (9, 14) days and 11 (9, 14) days before January 25 th and after and without significant difference. The time from exposure to definite diagnosis was 11 (9, 13) days in first-tier cities and 13 (11, 15) days in second and third-tier cities. The difference was significantly shorter of first-tier cities(U=1355.5,P=0.039). And also the time was short from visiting to definite diagnosis which was 2(2,3)days in first-tier cities and 3 (2, 4) days in second and third-tier cities but without significant difference(U=842.5,P=0.054). Conclusions: From our study we found that the best upper respiratory tract sampling time for novel coronavirus pneumonia suspects was 13days after exposure. The time from onset to definite diagnosis was shorter after January 25 th . The patients were diagnosed faster in the first-tier cities after exposure. Key Words: COVID-19 ,nucleic acid detection, exposure, sampling time Novel coronavirus infected patients with pneumonia have been discovered in Wuhan, Hubei since at the end of the December 2019. The epidemic has spread all of the the country and the wold make a great threat to the public health. There were 114 countries had infected patients and 118 000 patients in total until March 11 th with a mortality of 3.6%. The first sequencing of the viral RNA gene was completed in January 3rd by Chinese microbiologists and medical experts. The CDC shared the new gene sequence of the coronavirus to the world in January 10 th . They developed and tested PCR diagnostic reagent which was wildly used in clinic since January 11 th [1] .The novel coronavirus pneumonia was caused by novel coronavirus (2019-nCOV) which was renamed as SARS-CoV-2 in February 11 th by the the International Committee on Taxonomy of Viruses. SARS-CoV-2 belongs to the novel coronavirus of beta genus, with capsule, round or oval, 60-140nm in diameter and positive RNA virus. In vitro, sars-cov-2 can be found in human respiratory epithelial cells in about 96 hours [2] . Early novel coronavirus pneumonia patients had a history of Wuhan residence or contacted with the people from Wuhan, suggesting that there was interpersonal transmission [3, 4] . Covid-19 is a highly infectious disease. The R0 of covid-19 in early literature is 2.2 ~ 2.9 [1,5] and 3.77 in another study including 8 866 patients [6] . Therefore, early diagnosis, isolation and treatment of suspected cases are essential to control the epidemic. The detection of novel coronavirus nucleic acid is an effective method for rapid diagnosis [7, 8] . However when is the optimal upper respiratory tract sampling time is not sure. The optimal sampling time can help us to diagnosis in time at the same time to avoid the waste of the medical resources. In this study, we analyzed the distribution of the first positive time after exposure . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 9, 2020. . from different cities in order to obtain the optimal optimal upper respiratory tract sampling time. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. . the confirmed visiting time in fist tier city group was 72 cases and 89 cases in second tier and third tier city group. Statistical analysis: Statistical analyses were performed using SPSS 23.0 (International Business Machines Corporation, IBM, USA). Normally distributed . Normally distributed continuous variables are summarized as the mean and standard deviation and t-test was applied to test differences between two groups; Non-normally distributed data are recorded as median and interquartile range (Q25, Q75) as appropriate.，and U-test was applied to test differences between two groups; P < 0.05 was statistically significant. There were 136 (53.1%) cases were male and 120(46.9%) female, the average age was 43.80 ± 14.85 years old, most of them were between 31 and 70 years old (80.9%). . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. The median incubation period was 5 (3, 8) 17 . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. There was no significant difference between the two groups in age, gender and the time from exposure to diagnosis between patients before January 25 th and after. But the median time from onset to diagnosis was 5(3,7) days before January 25 th which was significantly shorter than 7.5(5,10) days(U=3885.5，P<0.001) ( Table 2) . . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. The age of onset was younger and the proportion of females was lager in the first tier cities. The median time from exposure to diagnosis was 11(9,13)days which was significantly shorter than 13 (11, 15 )days in the second and third tier cities group(U = 1355.5, P = 0.039). The median time from visiting to diagnosis was 2(2,3) days which was fast than 3(2,4)days in the second and third tier cities but without significant difference(U=842.5，P=0.054) ( Table 3) . Note: P < 0.05 is significant . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. . https://doi.org/10.1101/2020.05.06.20069302 doi: medRxiv preprint Novel coronavirus pneumonia is infectious at the early stage of onset. 96 hours when isolated and cultured in vitro [2] . The load of viral nucleic acid reached the peak within 2-5 days after the onset of the disease while the load of previous SARS CoV viral reached the peak about 10 days after the symptoms appeared [9] . Real time fluorescent RT-PCR is the most commonly used diagnostic method at present which amplify the specific nucleic acid sequence in the specimen. After more than 40 times of amplification, the quantity of nucleic acid can reach enough to be detected by conventional methods such as fluorescence. In this study, 136(52.9%) male patients were more than female which might be the reason that expression of ACE2 was higher in Asian men [10, 11] . There were 80.9% patients distributed from 31 to 70 years old which was similar to the study of the center of Disease Control and Prevention [12] . The incubation period of infectious diseases refers to the time from the entry of pathogenic microorganisms into the human body to the first symptoms of infection, which is an important basis for the isolation time limit of close contacts. The incubation period of new coronavirus is usually 1-14 days longer than that of SARS CoV for 2-10 days and mostly 3-7 days. In our study the incubation period was 0~18d, median time was 5 (3, 8) days,mean time was 5.5days and mode number was 4days which was similar as Li reported the retrospective research of the early stage of the epidemic including 425 patients [1] . However the cases involved in our study were all single exposure with a time span no more than 1day. There were 161 cases with confirmed visiting time, though the analysis of these patients the median time from visiting to diagnosis was 3(2,4)days and mode number was 2days. Although the time from visiting to diagnosis was in lager span time from 0 to 11days, only 7 cases were more than 6days, mainly concentrated in 0-6days. The reason for delay diagnosis may be due to the shortage of medical resources in some hospitals, on the other hand the . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted May 9, 2020. . https://doi.org/10.1101/2020.05.06.20069302 doi: medRxiv preprint early diagnosis of the disease should be confirmed by the expert of Health Commission. And finally the false negative of nucleic acid test of respiratory could also cause the delay diagnosis. The time from exposure to diagnosis of 256 patients was from 4 to 21 days, the median time was 11 (9, 14) days and mode number was 13 days. There were also several mainly reasons. First of all, the patients would not actively to see the doctor because of no evident symptoms during incubation period. And then due to the sensitivity of nucleic acid detection and sample quality the positive rate of pharyngeal sample nucleic acid detection might be less than 50% [13] . The positive rate may be higher of the sample form lower respiratory tract(sputum and bronchoalveolar lavage). However at the early stage of the disease the lesion is usually located in the lateral zone of the lung with the presentation of dry cough which cause the difficulty to obtain the sample form lower respiratory tract. At the early stage of infection the lower load of viral from upper respiratory tract was another reason leads to false negative test. We divided groups into before January 25 th and after because the first level response of major public health event was launched successively in most regions of the country from January 23 th to 25 th . We found that the median time from exposure to diagnosis was no significance between two groups but the median time from onset to diagnosis was significantly longer before January 25 th group. It was mainly because of the rapid response of the Chinese government to take many strategies including publish epidemic news, providing enough medical resources and so on. In such case, the patient would go to hospital as soon as they had the symptoms. The median time from onset to diagnosis was significantly shorter after January 25th group. The optimal upper respiratory tract sampling time from our study was 13 days after exposure. However the sample of our study was small, further larger sample is needed. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted May 9, 2020. . https://doi.org/10.1101/2020.05.06.20069302 doi: medRxiv preprint The data used to support the findings of this study are available from the corresponding author upon request. Early Transmission Dynamics in Wuhan, China, of Novel Coronavirus-Infected Pneumonia A Novel Coronavirus from Patients with Pneumonia in China A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster A familial cluster of infection associated with the 2019 novel coronavirus indicating potential person-to-person transmission during the incubation period Time-varying transmission dynamics of Novel Coronavirus Pneumonia in China Epidemiological and clinical features of the 2019 novel coronavirus outbreak in China Molecular Diagnosis of a Novel Coronavirus (2019-nCoV) Causing an Outbreak of Pneumonia Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR SARS-CoV-2 Viral Load in Upper Respiratory Specimens of Infected Patients Comparative genetic analysis of the novel coronavirus (2019-nCoV/SARS-CoV-2) receptor ACE2 in different populations Single-cell RNA expression profiling of ACE2, the putative receptor of Wuhan 2019-nCov The epidemiological characteristics of an outbreak of 2019 novel coronavirus diseases (COVID-19) in China Efficient management of novel coronavirus pneumonia by efficient prevention and control in scientific manner This work was supported by the Jinhua Science and Technology Bureau (2020XG-06) . The ethics committee of the hospital approved the study