Abstract: Objective To study the clinical application effect of modified nasopharyngeal swab sampling for 2019 novel coronavirus nucleic acid detection. Methods This study covered the period from January 14 to March 1, 2020.The supine position method and the protective face screen were used to collect nasopharyngeal swabs from February 24 onwards, before which, the nasopharyngeal swabs were collected by sitting position method. All the patients who were diagnosed with suspected/confirmed 2019 novel coronavirus infection were admitted from February 19 with the nasopharyngeal swabs collected outside the hospital before admission. (1) Thirty-four swabbing operators meeting the inclusion criteria of the study were recruited in this retrospective cohort study. They were grouped according to the collection method of nasopharyngeal swabs. Sixteen operators of Wuhan Taikang Tongji Hospital who applied the supine position method and the protective face screen were included in supine position method+ protective face screen group (15 males and 1 female, aged 34-49 years); 18 operators (12 from the First Affiliated Hospital of Army Medical University (the Third Military Medical University), 1 from Wuhan Jiangxia Mobile Cabin Hospital, 5 from the East District of People′s Hospital of Wuhan University) who applied the traditional sitting position method were included in sitting position method group (2 males and 16 females, aged 25-49 years). In supine position method+ protective face screen group, when collecting sample, the patient lay flat and wore a special protective face screen for nasopharyngeal swab sampling, with neck slightly extending and face turning to the opposite side of the operator about 10°. The self-designed questionnaire was used to investigate the cooperation, the incidence of nausea, coughing, sneezing, and struggling of patients evaluated by the operators, the operation time for a single swab sample, the fear of operation and the perceived exposure risk of operators in the two groups. (2) Sixty-five patients (22 males and 43 females, aged 25-91 years) admitted to Wuhan Taikang Tongji Hospital who successively received the sitting position method and supine position method+ protective face screen for nasopharyngeal swabs sampling and with complete nucleic acid detection results were included. The positive rates of nucleic acid detection by the two sampling methods of nasopharyngeal swabs of the patients were statistically analyzed. (3) Forty-one patients who could express their feelings accurately were selected out of those 65 patients (12 males and 29 females, aged 27-83 years). The comfort of patients in the process of sampling by the two methods was investigated. (4) Thirty-four patients (10 males and 24 females, aged 25-83 years) with two or more consecutive negative results of nucleic acid detection of nasopharyngeal swabs by sitting position method were selected from the above 65 patients. The positive rate of nucleic acid detection of nasopharyngeal swab of patients by supine position method+ protective face screen, i. e. negative to positive rate was statistically analyzed. Data were statistically analyzed with t test, Wilcoxon signed rank test, and chi-square test. Results (1) Compared with those of sitting position method group, the cooperation score of patients evaluated by the operators in supine position method+ protective face screen group was significantly higher (Z=-4.928, P<0.01), the incidence of nausea, choking cough, sneezing, and struggling of patients evaluated by the operators, and the fear of operation score and the perceived exposure risk score of operators in supine position method+ protective face screen group were significantly lower (Z=-5.071, -5.046, -4.095, -4.397, -4.174, -5.049, P<0.01), and the operation time for a single swab sample in supine position method+ protective face screen group was significantly longer (t=223.17, P<0.01). (2) The positive rate of nucleic acid detection of nasopharyngeal swabs by supine position method+ protective face screen was 60.00% (39/65), which was obviously higher than 41.54% (27/65) by sitting position method (χ²=4.432, P<0.05). (3) The comfort score of the 41 patients during nasopharyngeal swabs sampling by supine position method+ protective face screen was significantly higher than that by sitting position method (Z=-5.319, P<0.01). (4) Of the 34 patients with two or more consecutive negative results of nucleic acid detection of nasopharyngeal swabs by sitting position method, the rate of negative to positive of nucleic acid detection was 26.47% (9/34) after sampling by supine position method+ protective face screen. Conclusions Compared with the traditional sitting position method, detection of 2019 novel coronavirus nucleic acids of nasopharyngeal swabs collected by supine method combined with protective face screen is worth promoting, because of its better comfort of patients, low exposure risk for operators, in addition to reducing in the false negative result to some extent, which may help reduce false recurrence of discharged patients.